Best Software for Bookkeepers for 2025 (Top11 Picks)

Bookkeeping doesn’t stop at balancing the books, it’s about managing clients, payroll, time tracking, and workflows to keep everything running smoothly. The right tools can make a massive difference, saving you time, improving accuracy, and streamlining your work.

Here’s a breakdown of the best software for bookkeepers, covering everything from accounting and reconciliation tools to time management, project tracking, and CRM software. We’ve also made a table to help you compare them at a glance.

Best Software for bookkeepers

• Xero + Link My Books 
• QuickBooks with Link My Books 
• Multiview 
• Hubdoc 
• Expensify 
• Gusto 
• Wave 
• Zoho Books 
• Square
• FreeAgent 
• Striven

1. Xero + Link My Books – Best for e-commerce Bookkeeping Automation

Xero combined with Link My Books is a go-to for automating bookkeeping for e-commerce businesses. Link My Books integrates seamlessly with E-commerce platforms, pulling transaction data directly and automating reconciliation, tax reporting, and fee tracking.

Features

• Automated Transaction Import: Link My Books pulls sales, refunds, fees, and taxes directly from Amazon, Shopify, or eBay and categorizes them automatically into Xero.
• Perfect Payout Matching: Generates payout summaries that match bank deposits exactly, saving hours of manual reconciliation work.
• Multi-Currency Handling: Supports sellers operating internationally by automatically converting foreign sales into your base currency using accurate exchange rates.
• Tax Compliance: Automatically applies correct tax treatments, including sales tax, VAT, or GST, ensuring error-free reporting.
• Financial Analytics: Provides reports on profit, margins, and costs to give bookkeepers and clients a clear understanding of business performance.

Benefits

For bookkeepers working with high-transaction eCommerce clients, this setup eliminates manual errors, speeds up month-end processes, and ensures tax-ready financials effortlessly. This powerful integration does more than just automate bookkeeping, it transforms how bookkeepers work:

• Saves Hours of Manual Work: Automation handles the heavy lifting, allowing bookkeepers to focus on higher-value tasks.
• Eliminates Errors: Accurate data flows directly into Xero, reducing human errors and improving confidence in financial reporting.
• Streamlines Workflows: Seamless integration means fewer tools to juggle and smoother processes overall.
• Delivers Better Insights: Bookkeepers can provide clients with clear financial visibility, tax readiness, and actionable profitability insights.

Link My Books & Xero = Error free accounting

This combo is ideal for e-commerce bookkeeping automation, it offers seamless integration with multiple sales channels, accurate tax compliance, and efficient cost of goods sold (COGS) tracking. Designed specifically for e-commerce sellers and their bookkeepers, this integration transforms complex financial tasks into seamless, automated workflows.

Ready to make e-commerce bookkeeping effortless?

Start your free trial of Link My Books today! 🚀

2. QuickBooks with Link My Books - Best for High Volume E-commerce Bookkeepers

QuickBooks Online paired with Link My Books simplifies reconciliation for e-commerce sellers while offering advanced financial insights. This duo handles complex transaction data, fee tracking, and sales tax, all while providing in-depth customizable reports.

Features

• Seamless Integration: Link My Books connects directly to QuickBooks, pulling in all sales, fees, refunds, and taxes. Transactions are cleanly organized and sent to QuickBooks for automatic reconciliation.
• Customizable Reporting: Generate detailed reports for profit and loss, tax liability, and cost of goods sold (COGS). Customize reports to deliver actionable insights for clients.
• Multi-Channel Reconciliation: Handles multiple platforms (Amazon, Shopify, Etsy) seamlessly, ensuring data accuracy across channels.
• Scalability: Easily handles thousands of transactions, making it perfect for businesses with large sales volumes.

Benefits

This integration is perfect for bookkeepers who need detailed reporting and analytics for their clients. These robust reporting tools enable better forecasting, financial analysis, and performance tracking for clients scaling their businesses.

• Efficient Financial Management: Provides a range of features for comprehensive financial management.
• Operational Efficiency: Enhances operational efficiency by automating tasks and providing insights.
• Compliance and Security: Ensures compliance with tax laws and contributes to the security of financial data.

Link My Books & Quickbooks = Advanced Reporting 

Best for advanced reporting and scalability, this duo provides custom reporting features, multi-currency support, and comprehensive tax compliance, making it suitable for managing growing businesses.

Read more about the best sales tax software for ecommerce.

Multiview ERP – Best for Enterprise Accounting Solutions

Multiview offers a robust accounting platform with advanced features for financial management, reporting, and budgeting. It’s ideal for enterprise-level clients who need comprehensive accounting support.

It supports integration with popular e-commerce platforms like Shopify, Amazon, and eBay.

Features

• Multi-Entity Financial Management: Consolidates data for businesses operating in multiple locations or managing multiple subsidiaries.
• Customizable Dashboards: Tailor real-time dashboards to track KPIs, budgets, and financial health at a glance.
• Expense and Budget Management: Track expenses, compare against budgets, and analyze spending trends to optimize cash flow.
• Audit-Ready Reporting: Generates detailed financial reports, supporting compliance and year-end audits.
• Multi-Currency Support: Handles global operations with accurate currency conversion and reporting.

Multiview gives bookkeepers enterprise-grade tools to manage complex financials and deliver detailed insights to larger clients.

Hubdoc – Best for Document Management and Receipt Automation

Hubdoc automates the collection and organization of financial documents, saving bookkeepers time and hassle. It syncs seamlessly with Xero and QuickBooks, ensuring receipts, bills, and statements are stored and reconciled correctly.

Features

• Automated Document Collection: Pulls bills and bank statements from connected accounts.
• Receipt Scanning: Upload receipts using your phone or email for automatic extraction.
• Sync with Accounting Software: Sends documents directly to Xero or QuickBooks.
• Searchable Storage: All files are organized and easily searchable.

Hubdoc eliminates the need for manual data entry and keeps client records tidy and audit-ready. It's great for bookkeepers drowning in receipts, invoices, and paperwork.

Expensify – Best for Expense Tracking and Management

Expensify makes it easy to track, categorize, and approve expenses. It integrates with various software, including accounting and finance tools, with this tool bookkeepers can ensure client spending is accounted for without chasing paperwork or receipts.

Features

• Automatic Expense Reports: Scans receipts and generates reports.
• Approval Workflows: Streamlines approval processes for teams.
• Real-Time Tracking: Track expenses and reimbursements instantly.
• Credit Card Integration: Syncs with company cards to simplify expense matching.

Expensify simplifies expense management for clients, and bookkeepers get clean, organized data for reporting. It’s great for bookkeepers helping clients manage business expenses.

Gusto – Best for Payroll Processing

Gusto is an all-in-one payroll software that simplifies payroll processing, tax filing, and benefits management. It’s designed for small to mid-sized businesses and integrates with major accounting software, it integrates with platforms like Zoho Books. 

Features

• Automated Payroll: Runs payroll, calculates taxes, and files automatically.
• Benefits Management: Handles health insurance, 401(k), and other employee benefits.
• Employee Self-Service: Employees can access pay stubs and tax documents.
• Time Tracking Integration: Syncs hours worked for accurate payroll.

Gusto ensures payroll accuracy, simplifies tax filing, and reduces manual work for bookkeepers. It’s great for bookkeepers managing payroll and HR for clients.

Wave – Best Free Bookkeeping Software for Small Businesses

Wave offers free accounting tools, including invoicing, bookkeeping, and expense management. While it’s not as feature-rich as premium software, it’s a great choice for small clients. Wave partners with Zoho Books for users outside the U.S. and Canada.

Features

• Free Invoicing and Accounting: No-cost bookkeeping and invoicing tools.
• Bank Reconciliation: Connects to bank accounts for simple reconciliation.
• Expense Tracking: Categorizes and organizes expenses automatically.

For smaller clients, Wave is an affordable, simple bookkeeping solution. It’s great for bookkeepers helping freelancers or micro-businesses on a tight budget.

Zoho Books – Best for Growing Small Businesses

Zoho Books is ideal for businesses scaling their operations. With advanced automation, bank reconciliation, and integration capabilities, Zoho Books simplifies reconciliation while supporting multi-currency and multi-channel operations. It also offers direct integration with e-commerce platforms like Square.

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Features

• Bank Reconciliation: Matches transactions with bank records.
• Inventory Management: Tracks stock and sales.
• Customizable Reports: Generates tailored financial reports.

This platform works great for bookkeepers serving growing businesses that need scalability.

Square – Best for POS and Payment Tracking

Square is a versatile solution for payment processing and point of sale (POS), ensuring businesses can efficiently manage transactions and inventory. It allows businesses to accept payments, track sales, manage inventory, and analyze business trends. It includes tools for employee management, and customer engagement, and integrates with various business software for seamless operations. 

Features

• Payment Processing: Accepts payments in-store, online, and on-the-go.
• Point of Sale (POS) System: Manages inventory, employees, and customers.
• Invoice and Estimates: Sends professional invoices and estimates.
• Integration with e-commerce Platforms: Works seamlessly with various e-commerce platforms.

If you are looking for the best accounting software for Square, consider Xero or QuickBooks combined with Link My Books.

FreeAgent – Best for Freelancers and Micro-Businesses

Designed for freelancers and micro-businesses, FreeAgent offers invoicing, expense tracking, and time tracking features, simplifying financial tasks for small-scale operations.

Features

• Invoicing and Estimates: Send customized invoices and track payments easily.
• Expense Tracking: Manage expenses and upload receipts on the go.
• Time Tracking: Log billable hours and link them to client invoices.

FreeAgent’s simplicity makes it ideal for bookkeepers supporting freelancers or micro-businesses with straightforward accounting needs.

Striven – Best All-in-One Business Management Software

Striven encompasses accounting, inventory management, HR, and CRM tools, providing a comprehensive platform for various industries and organization sizes.

Features

• Accounting: Complete bookkeeping features, including invoicing and reconciliation.
• Project Management: Track tasks, time, and budgets for client projects.
• CRM Integration: Manage client relationships and communication.
• Inventory and HR Tools: Monitor inventory, payroll, and employee performance.

Striven simplifies workflows by combining accounting with project and client management, making it ideal for bookkeepers juggling multiple roles. It's great for bookkeepers managing clients who need project management, accounting, and CRM tools in one place.

How to choose the best bookkeeping software for you

Choosing the right bookkeeping software is essential for efficient, accurate financial management. With so many tools available, the decision comes down to selecting software that aligns with your specific needs and improves your day-to-day bookkeeping processes. 

Here’s what you should look for to make the best choice:

1. Integration Capabilities

Integration is everything when it comes to bookkeeping software. The right tool should seamlessly connect with platforms you already use, like e-commerce platforms (Amazon, Shopify, eBay), payment gateways, and CRM systems. This is necessary for multichannel ecommerce accounting. 

Smooth integrations ensure that:

• Data flows effortlessly between systems.
• Manual data entry is minimized, saving hours of work.
• Your workflow stays efficient and streamlined.

Integrations help bookkeepers manage complex tasks across platforms, particularly for clients in retail, e-commerce, or businesses that rely on multiple tools.

2. Ease of Use and User Experience

Nobody wants software that’s clunky or hard to navigate. A clean, intuitive interface ensures that you can find features quickly and get tasks done efficiently. Consider:

• How easy it is to set up and navigate the software.
• Whether there are training resources or onboarding support.
• How well the tool integrates into your daily workflow.

Software that’s user-friendly saves time, reduces errors, and makes the bookkeeping experience far more productive.

3. Customization and Scalability

Your software should work for you, not the other way around. Look for tools that can be tailored to your specific needs and grow with your business. Key areas to evaluate include:

• Customization: Can you adjust reports, dashboards, or workflows to match your requirements?
• Scalability: Will the software still work as your client base grows or as businesses scale up?

Bookkeepers need software that adapts to different industries, client needs, and business complexities without outgrowing its usefulness.

Read more about the top 10 accounting software for large companies.

4. Compliance and Security

When dealing with financial data, compliance and security are non-negotiable. Choose software that helps you stay on top of regulatory requirements and ensures data is protected. Key features include:

• Data Security: Encryption, two-factor authentication, and automatic backups to protect sensitive data.
• Compliance Tools: Support for tax regulations, payroll laws, and financial reporting standards.
• User Permissions: Control access to sensitive data for clients or team members.

Secure, compliant software gives bookkeepers peace of mind, ensuring their clients' financial data is accurate, protected, and audit-ready.

5. Cost-Efficiency and Value

Cost is important, but it’s about value, not just price. Evaluate what you’re getting for your investment:

• Are the core features worth the cost?
• Does the software reduce manual work and save you time?
• Are there hidden costs for upgrades, support, or additional features?

Investing in the right software pays off through saved time, fewer errors, and better financial insights, far outweighing the upfront cost.

6. e-commerce-Specific Features

If you’re handling e-commerce clients, specialized features are a must. Look for tools that:

• Integrate directly with platforms like Amazon, Shopify, or Etsy.
• Automatically track sales, refunds, and fees.
• Manage taxes like VAT or GST for online transactions.

E-commerce bookkeeping can get messy quickly. Look for accounting automation software with these features that simplifies reconciliation, reporting, and tax compliance.

7. Customer Support

Even the best software can hit a snag. Reliable, responsive customer support makes a huge difference, especially when deadlines are tight. Look for:

• Live chat, phone, or email support options.
• Knowledge bases, FAQs, or training resources.
• Onboarding support for complex setups.

Fast, effective support keeps your bookkeeping workflow running smoothly and prevents time-consuming roadblocks.

How do They Compare

We’ve made a comparison table to help you see how they measure up at a glance. 

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Why accounting software alone is not enough for modern bookkeepers?

Modern bookkeeping isn’t just about recording numbers, it’s about managing increasingly complex financial data across multiple platforms. While traditional accounting software like Xero or QuickBooks is essential for organizing and reporting finances, it isn’t enough on its own to meet the demands of modern bookkeepers, especially those working with eCommerce businesses or clients with diverse revenue streams.

Today’s bookkeepers handle more than just ledgers and spreadsheets. They’re tasked with managing:

• High Transaction Volumes: Businesses, especially in e-commerce, process hundreds or thousands of sales, refunds, and fees every month.
• Multi-Platform Sales: Clients sell across platforms like Amazon, Shopify, Etsy, and eBay, creating fragmented data.
• Complex Reconciliations: Payments from platforms like Amazon include sales, fees, refunds, and taxes in a single payout, making manual reconciliation a headache.
• Tax Compliance: Sales tax, VAT, and GST differ across regions and platforms, requiring precise calculations and reporting.

If you rely on accounting software alone, you’ll spend hours manually sorting through data, importing transactions, and reconciling bank deposits, time that could be better spent providing insights and value to your clients.

Why do e-commerce bookkeepers choose Link My Books?

The combination of Link My Books and leading e-commerce accounting software like Xero or QuickBooks is a must-have for modern e-commerce bookkeeping. Designed specifically to handle the unique challenges of online sellers, this integration delivers unmatched accuracy, efficiency, and reliability while simplifying complex workflows.

Here’s why bookkeepers trust Link My Books to streamline e-commerce bookkeeping and ensure error-free accounting:

1. Seamless Integration with Multiple Sales Channels

Managing sales data from platforms like Amazon, Shopify, eBay, and Etsy can quickly become a nightmare. Each platform generates its own mix of sales, refunds, fees, and taxes, often leaving bookkeepers to manually piece together fragmented data.

What Link My Books Does:

• Automatically imports all transaction data directly from sales platforms.
• Organizes sales, refunds, and fees into clean, categorized summaries.
• Syncs this data seamlessly into your accounting software.

Why It Matters:

• Eliminates hours of manual data entry
• Reduces the risk of human error by automating categorization
• Allows bookkeepers to manage multiple platforms from a single system

2. Accurate Tax Compliance

Tax compliance, whether for sales tax, VAT, or GST, is one of the most complex aspects of e-commerce bookkeeping. Manual calculations often lead to mistakes, risking fines or inaccurate reporting.

What Link My Books Does:

• Automatically applies the correct tax treatments for every transaction.
• Categorizes and summarizes all sales taxes, VAT, and GST by region.
• Generates tax-ready summaries to make reporting and filing simple.

Why It Matters:

• Ensures compliance with local and international tax regulations
• Saves bookkeepers hours of manual tax reconciliation
• Reduces the risk of costly penalties or underreporting

3. Efficient Cost of Goods Sold (COGS) Tracking

Tracking COGS is essential for understanding profitability, but managing inventory costs for eCommerce clients can be overwhelming, especially with high transaction volumes.

What Link My Books Does:

• Automatically calculates and tracks COGS for every sale.
• Pulls product cost data and allocates it directly to transactions in your accounting software.
• Provides clear visibility into margins and profit.

Why It Matters:

• Bookkeepers can monitor gross profit and help clients optimize pricing and costs
• Ensures accurate financial statements that reflect true profitability
• Simplifies inventory accounting, even as transaction volumes scale

4. Simplified Reconciliation

Reconciling e-commerce payouts is one of the most time-consuming and error-prone tasks for bookkeepers. Sales platforms like Amazon combine multiple components, sales, refunds, fees, and taxes, into single deposits, which rarely match up perfectly with bank feeds.

What Link My Books Does:

• Breaks down complex payouts into clean, accurate summaries.
• Matches transactions seamlessly with bank deposits in your accounting software.
• Automates reconciliation with just one click.

Why It Matters:

• Saves hours of manual reconciliation work
• Ensures every dollar is accounted for without discrepancies
• Provides clean, audit-ready financial data

5. Scalability Without Compromise

As e-commerce businesses grow, bookkeeping becomes increasingly complex. More sales channels, higher transaction volumes, and multi-currency operations can quickly overwhelm manual processes.

What Link My Books Offers:

• Effortlessly handles thousands of transactions across multiple platforms.
• Automated workflows scale alongside growing businesses.
• Maintains consistent accuracy, no matter how complex the operation becomes.

Why It Matters:

• Bookkeepers can confidently support growing businesses without added workload.
• Clients get reliable financial data, even as sales volumes expand.
• No compromise on efficiency, accuracy, or workflow management.

FAQ

1. What are the typical costs associated with bookkeeping software?

Some software offers free basic versions, while others require a monthly subscription, usually from $10 to $50. High-end solutions may cost more but provide advanced features and flexible plans.

With Link My Books, you can set up a demo or activate a 14-day free trial before settling for one of the three payment tiers. Use our calculator to set your estimated monthly orders and see the prices.

2. What are the differences between desktop and online bookkeeping software?

Desktop software is installed on your computer and stores data locally. It's usually more secure but less flexible. 

On the other hand, Link My Books is an online software that is accessible from any device with an internet connection. It offers more flexibility and real-time updates but relies on internet connectivity.

3. Can bookkeeping software iIntegrate with other Business tools?

Yes, most bookkeeping software can integrate with other business tools, such as invoicing, payroll systems, and banking platforms. This streamlines your workflow, making it easier to manage all your financial tasks in one place.

Link My Books offers you a wide range of integrations, including:

• Amazon to Xero
• eBay to QuickBooks
• Etsy to Xero
• Shopify to Xero
• Walmart to Xero

4. What accounting integrations should I consider when choosing bookkeeping software?

When selecting bookkeeping software, prioritize integrations that align with your needs. Integrations that streamline workflows and reduce manual work are key. Here’s where Link My Books shines:

• Seamless e-commerce Sync: Direct integrations with Amazon, Shopify, eBay, and Etsy pull in all sales, fees, refunds, and taxes automatically.
• Error-Free Bank Reconciliation: Matches complex eCommerce payouts perfectly with bank deposits in Xero or QuickBooks.
• Automated Tax Compliance: Applies accurate tax treatments (VAT, GST, sales tax) and generates tax-ready summaries.
• Expense Tracking: Automatically categorizes platform fees and refunds, saving hours of manual work.
• Real-Time Insights: Provides clear profitability and COGS tracking without extra reporting tools.

The more integrated your system, the more efficient and accurate your bookkeeping processes will be.

5. How can cloud-based bookkeeping software help me manage my clients finances more efficiently?

Cloud-based bookkeeping software offers a range of benefits that improve efficiency and accuracy:

• Remote Accessibility: Manage your clients’ finances from anywhere, anytime, without being tied to an office computer.
• Automation: Automatically sync transactions, reconcile bank feeds, and categorize expenses, saving hours of manual work.
• Real-Time Data: Cloud software provides up-to-date financial information, allowing bookkeepers to identify and resolve issues faster.
• Collaboration: Multiple users can access and edit financial data in real-time, improving client communication and teamwork.
• Data Security: Cloud solutions use encryption and automatic backups to protect sensitive financial information.
• Scalability: Easily add more clients, integrate new tools, or upgrade features as your bookkeeping practice grows.

Cloud-based tools like Link My Books allow bookkeepers to handle more clients, reduce errors, and provide real-time financial insights, all while working smarter, not harder.

Which software is best for your bookkeeping practice?

To save you time, we’ve cut through the clutter and reviewed different software options based on their ease of use, the features they offer, the metrics they track, and which businesses they're best suited for. 

Here’s a quick summary:

If you’re managing e-commerce clients, go for Xero or QuickBooks paired with Link My Books, it’s the ultimate solution for automating sales tracking, tax compliance, and reconciliation across platforms like Amazon, Shopify, and eBay.

For bookkeepers working with small businesses or startups, Zoho Books offers affordability and customization, while Wave works well for freelancers needing basic, free accounting tools.

If you focus on expense management, Expensify is your go-to for automating receipt scanning and approvals, and Hubdoc shines for managing bills and documents.

If you just need a payroll solution, look no further than Gusto, which handles payroll, taxes, and benefits seamlessly.

For larger, enterprise-level clients, consider Multiview or Striven, which offer advanced reporting, multi-entity management, and all-in-one business solutions.

Simplify e-commerce accounting with Link My Books

Bookkeeping requires more than just traditional accounting software. To stay efficient, accurate, and competitive, you need tools that integrate seamlessly with the platforms your clients use, like Amazon, Shopify, and Etsy.

Link My Books complements Xero and QuickBooks by automating data import, simplifying reconciliation, and ensuring compliance, allowing you to:

• Eliminate manual work
• Save hours of time
• Provide better insights and value to their clients

Link My Books doesn’t replace accounting software it makes it smarter, faster, and far more powerful.

Ready to automate your bookkeeping?

It will take you only 15 minutes to set it up and you can try it for 14 days completely free.Start your free trial of Link My Books today and see the difference! 🚀

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