Best Accounting Software for Square

The Square platform offers excellent tools for sales, but when it comes to detailed accounting, many sellers find themselves struggling with manual data entry, tax calculations, and ensuring compliance with different regulations. These challenges can not only consume your time but also lead to costly errors. 

This is where integrating the right accounting software comes into play, offering automation, accuracy, and peace of mind.

We’ve compared the best accounting software for Square to make finding the right one for your business easy. You can also see a comparison table for a quick overview. 

Best Accounting Software for Square 

• Xero with Link My Books
• QuickBooks Online with Link My Books
• Zoho Books
• Sage Business Cloud Accounting
• FreshBooks
• Wave

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We’ll explore the top features of each software in this article. Or you can try out Link My Books right away and see the benefits for yourself.

Xero with Link My Books

Xero is a great choice for Square sellers, especially when integrated with Link My Books. This combination ensures error-free accounting by automating the reconciliation of your sales, fees, and taxes, making your financial management as seamless as possible.

Xero Features

• Automated Data Sync: Xero automatically syncs with Square through Link My Books, importing all sales, refunds, and fees directly into your accounting system. This eliminates manual entry and reduces the risk of errors, streamlining your financial processes.
• Accurate Tax Management: Xero helps Square sellers handle complex tax scenarios with ease, applying the correct tax rates and ensuring compliance across multiple regions. This is crucial for businesses operating in different tax jurisdictions.
• Multi-Channel Support: Xero excels in multi-channel management, allowing sellers who operate across various platforms like Square, eBay, and WooCommerce to maintain accurate, unified financial records.
• Seamless Integration with Third-Party Apps: Xero integrates with over 1,000 third-party apps, including e-commerce, inventory management, and CRM tools, allowing you to manage all aspects of your business from one central platform.

Link My Books + Xero = Error-free Accounting

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Link My Books seamlessly connects your business with Xero so you can count on your books always being in order. It automates the entire process, validating each transaction, ensuring accurate tax application, and simplifying reconciliation with one-click matching. Plus, it offers deeper insights like cost tracking and benchmarking. Link My Books provides a more robust, hassle-free experience that’s better suited for managing your Square sales.

How Does it Work?

1. Connect your Square account to Xero via Link My Books.

2. With each Square payout, Link My Books verifies all transactions, ensuring that every order is treated correctly for tax purposes.

3. Link My Books then creates a detailed summary invoice in Xero, itemizing the payout into sales, refunds, and fees, and assigning them to the proper accounts with the correct tax rates.

4. The Xero entry matches effortlessly with the bank deposit in a single click.

The integration takes 15 minutes to set up and you can try it out for 14 days, free of charge. 

Xero Pricing

For US Customers

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For UK Customers

While Xero’s Ignite plan is budget-friendly, it does come with some limitations, like only allowing 20 invoices and 10 bills per month. This is fine if you have only a few clients and you just need the basics from your Walmart bookkeeping software.

If your business is growing, you might want to upgrade to Grow, which offers more flexibility. And if you deal with multiple currencies, the Comprehensive plan has you covered

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For AU Customers 

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QuickBooks with Link My Books

QuickBooks Online is an excellent option for Square sellers, especially when integrated with Link My Books. It automates data entry, categorizes transactions, and ensures accurate tax calculations.

QuickBooks Online Features

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• Automatic Transaction Import: QuickBooks Online connects with Square via Link My Books to automatically import transaction data, including sales, refunds, and fees. This feature significantly reduces manual data entry and simplifies bookkeeping.
• Customizable Class Tracking: This feature allows you to categorize transactions by different segments, such as product lines or sales channels. Link My Books enhances this by automatically assigning transactions to the correct classes, ensuring your profit and loss (P&L) statements are detailed and accurate.
• Advanced Reconciliation Tools: QuickBooks makes bank reconciliation easy by matching your Square payouts with corresponding bank deposits. With one-click reconciliation, you can ensure that your records are always accurate and up-to-date.

You can connect Square directly to QuickBooks Online through the Square by Commerce Sync app. 

This setup automatically downloads your Square sales into QuickBooks. However, the app has some limitations:

• It doesn’t import customer details like names or emails from Square into QuickBooks.
• If you manage multiple business locations, the app only tracks transactions for one location. You’d need to manually separate transactions for different locations in QuickBooks.
• QuickBooks downloads new transactions daily, but it doesn’t provide a summary view of all your daily transactions.
• Square can only sync with one QuickBooks Online account, and once connected, you can’t import the transactions into another account.

While this setup is useful, Link My Books offers a better solution. 

Link My Books & Quickbooks = Advanced Reporting 

Unlike the Commerce Sync app, Link My Books provides full transaction summaries, supports multi-location management, and automatically validates and reconciles transactions, ensuring accuracy and saving you time. Plus, it handles Square fees and tax applications seamlessly, giving you more control and better insights into your finances.

It takes only one click to reconcile all your payments. And you can easily track your cost of goods sold, ensuring that your profit margins are always accurate.

Try out our integration with QuickBooks and let Link My Books simplify your Square accounting. You can set it up in 15 minutes, and try it out for 14 days, free of charge.

QuickBooks Online Pricing

For US Customers

*The image is reflecting a current discount

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For UK Customers

*The image reflects a current offer, buy now & save 90% for 6 months

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Simple Start is best for freelancers and very small businesses with minimal accounting needs. Essentials suits small businesses that require basic features plus bill management and time tracking. Plus is ideal for businesses that need to manage inventory and track project profitability.

Advanced is designed for larger businesses that need advanced reporting, more users, and premium support.

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For AU Customers 

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Zoho Books

Zoho Books simplifies accounting for Square sellers with automated workflows and robust tax compliance features.

Zoho Books Features 

• Multi-Currency Support: Zoho Books supports multi-currency transactions, automatically updating exchange rates, which is essential for Square sellers with an international customer base.
• Automated Workflows: This feature allows you to automate routine tasks such as invoicing, payment reminders, and inventory updates, helping you save time and reduce errors.
• Inventory Management: Zoho Books includes robust inventory management tools, keeping track of stock levels, alerting you when inventory is low, and helping you manage reorders.

You can integrate Square with Zoho Books directly. To do this you need to integrate Square as an online payment gateway within the Zoho Books platform. This allows you to automatically sync your sales transactions from Square into Zoho Books, where you can track payments, manage refunds, and reconcile accounts. 

The setup involves linking your Square account to Zoho Books and configuring the payment settings to manage transactions. However, this is a lengthy process and you will need some accounting knowledge to do it correctly. 

Zoho Books Pricing

For US Customers

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For UK Customers

The Free Plan is for businesses with minimal accounting needs. Paid plans start at £12/month, offering additional features and higher limits.

For AU Customers 

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Sage Business Cloud Accounting

Sage Business Cloud Accounting offers a customizable dashboard and real-time data access, making it a good choice for Square sellers who need detailed financial insights. If you have more complex accounting needs, particularly if you’re managing larger inventories or need detailed financial reports, this might be a good choice.

Top Features of Sage

• Comprehensive Reporting: Sage provides detailed financial reports, including cash flow analysis and profitability reports, tailored to help you make informed business decisions.
• Inventory Tracking: With Sage, you can manage inventory across multiple channels, ensuring accurate stock levels and cost management. This feature is particularly useful for businesses with complex inventory needs.
• Multi-User Access: Sage allows multiple team members to access the accounting system with different levels of permissions, facilitating collaboration while maintaining control over sensitive financial information.

Sage Pricing

For US Customers 

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For UK Customers 

The Basic Package starts at £15/month, with additional features available on higher-tier plans.

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FreshBooks

FreshBooks offers an intuitive, user-friendly interface perfect for Square sellers who prioritize ease of use. It’s good for invoicing, tracking expenses, and managing client payments.

FreshBooks Features 

• Simplified Invoicing: FreshBooks offers easy-to-use invoicing tools that allow you to create professional invoices, automate recurring billing, and track payment statuses. This is ideal for small businesses and freelancers who need to streamline their billing processes.
• Expense Tracking: FreshBooks automatically categorizes and tracks expenses, helping you maintain a clear overview of your financial health. This feature is essential for keeping your budget on track and managing cash flow effectively.
• Time Tracking: For service-based businesses, FreshBooks includes a time-tracking feature that integrates seamlessly with invoicing, making it easy to bill clients accurately for hours worked.

You can integrate Square directly with FreshBooks. 

This integration automatically imports payments, sales, and fees, enabling you to generate invoices, track expenses, and manage customer payments within FreshBooks. 

Drawbacks:

• Limited Depth of Integration: The integration primarily focuses on importing basic transaction data, without offering advanced features like detailed financial analysis or automated tax calculations.
• Manual Reconciliation: While sales data is synced, the reconciliation of transactions with bank deposits may still require manual effort, as the integration does not automatically match these records.
• Potential for Data Gaps: The integration may not capture all nuanced details of Square transactions, such as tips, refunds, or multi-location data, requiring additional manual adjustments in FreshBooks.

FreshBooks Pricing

For US Customers

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For UK Customers

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FreshBooks offers four plans. Lite for freelancers with up to 5 clients, Plus for growing businesses with up to 50 clients, Premium for unlimited clients, and Select, a custom-priced option with advanced features and a dedicated account manager. Each plan includes essential tools like invoicing, expense tracking, and accounting.

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For AU Customers

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Wave

Wave is a free accounting solution that offers essential tools for small Square sellers, including invoicing and expense tracking.

Top Features of Wave

• Free Accounting Tools: Wave provides essential accounting features such as invoicing, expense tracking, and financial reporting at no cost. This makes it an attractive option for small businesses operating on a tight budget.
• Simple Interface: Wave’s user-friendly design is perfect for those who may not have extensive accounting experience. The clean layout simplifies managing your finances.
• Basic Integrations: While Wave offers basic integration with Square, it may not be as robust as paid options like Xero or QuickBooks. However, it’s sufficient for small businesses needing simple financial management.

Wave Pricing

Wave account sign-ups are limited to US and Canadian business owners only. Wawe doesn’t provide support for this product outside of this region.

• Free Plan: Wave offers free accounting services, including invoicing, billing, and expense tracking. Payroll is not included in the free plan.
• Payroll Add-On: Available as a paid service, where the pricing varies depending on the state. In tax-service states, Wave handles payroll taxes on your behalf, whereas in self-service states, you manage payroll taxes manually.

For US Customers

Wave’s basic accounting and invoicing tools are free, making it a good choice if you’re a budget-conscious seller. If you need more advanced features, you can upgrade to a monthly plan for $16/month.

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How to Choose the Best Square Bookkeeping Software for You

When selecting the right bookkeeping software for your Square-based business, you should consider several factors to ensure the software meets your needs. Here’s what to focus on:

Accuracy

Look for software that integrates seamlessly with Square, automating the import and categorization of sales, refunds, and fees. This minimizes manual entry and ensures that every transaction is recorded correctly. The software should also handle Square’s specific requirements, such as managing different payment types and applying the correct tax rates for each sale. 

Time-Saving Features

Time is a valuable resource for any business owner. The right bookkeeping software should offer automation features that save you time by reducing manual data entry, automating reconciliation, and providing real-time updates. This means choosing software that syncs automatically with Square, ensuring all sales data is up-to-date and accurately reflected in your books. 

E-commerce Specific Features

Your bookkeeping software should cater to your business. This includes features like multi-channel sales tracking, detailed sales reporting, and inventory management. It’s also important that the software handles the complexities of Square’s payment ecosystem, which includes both in-person and online sales. For businesses selling internationally, look for software that supports multi-currency transactions and automatic tax calculations.

Ease of Use

Even with powerful features, bookkeeping software needs to be user-friendly. Square sellers should look for software with an intuitive interface that’s easy to navigate. A straightforward setup process and minimal learning curve are also important, as well as easy access to customer support. The best software should make financial management easier, not more complicated.

Value for Money

Compare the pricing plans of different bookkeeping software and consider the value they offer for the price. Some tools offer free plans with basic features, which can be enough for small businesses. However, if you need advanced features like multi-location tracking or detailed financial analytics, investing in a more comprehensive solution is worth the extra cost.

Customer Support

Choose software that offers reliable support through various channels like live chat, email, or phone. It’s important that the support team understands the specific challenges of integrating with Square and can assist you when issues arise. Good support can make a significant difference in resolving problems quickly and keeping your business running smoothly.

Beyond the Features

Beyond basic bookkeeping, your software should offer valuable insights into your business’s performance in the e-commerce space. 

Look for tools that provide detailed financial analytics, including profit and loss statements, sales trends, and benchmarking against industry standards. These insights are vital for making informed decisions and staying competitive. 

How do They Compare?

Why Accounting Software Alone is Not Enough 

Using accounting software is necessary for managing your finances but for Square sellers, this might not cover all the complexities involved. Square is designed primarily for payment processing and POS (Point of Sale) operations. However, when it comes to detailed financial management, there are specific challenges that general accounting software may not fully address.

Complex integration needs: Square sellers often manage transactions across multiple channels and regions, which can complicate financial tracking. While accounting software like Xero or QuickBooks can handle basic bookkeeping, integrating these platforms with Square's detailed transaction data requires specialized tools like Link My Books. 

Tax compliance: Square sellers need to comply with various tax regulations, depending on their location and the regions they sell in. Accounting software alone might not handle the intricacies of tax calculations for different states or countries, especially with evolving tax laws. Advanced integrations can automate the application of correct tax rates and ensure accurate reporting, reducing the risk of non-compliance and penalties​

Multi-channel management: If you’re selling on Square alongside other platforms like Shopify or eBay, managing finances across these channels can be overwhelming. Accounting software might not fully support this multi-channel approach without additional tools. Integrations like Link My Books help consolidate financial data from all sales channels, providing a clearer financial picture and saving time on manual reconciliations​

Why do Square sellers choose Link My Books?

Square sellers who are looking to streamline their accounting choose Link My Books to maintain tax compliance, and gain deeper insights into their business’s financial health. 

Link My Books will give you benefits that go beyond what traditional accounting software can offer. It directly integrates with Square, automating the import of sales data, refunds, and fees into accounting software like Xero and QuickBooks. This integration reduces manual entry, minimizes errors, and saves time, making it easier to keep financial records accurate.

Link My Books Features 

Payout Reconciliation

Reconciling Square payments with bank deposits can be a tedious task. Link My Books simplifies this by automatically matching Square payouts with bank statements, ensuring all transactions are accounted for accurately. This feature reduces the time spent on reconciliation, making it a hassle-free process.

Financial Analytics

Link My Books provides real-time financial analytics, giving Square sellers insights into their business’s performance. This includes detailed reports on sales trends, profitability, and cash flow. With up-to-date data, sellers can make informed decisions quickly, helping them stay competitive and responsive to market changes.

Industry Benchmarking

Link My Books offers benchmarking tools that allow Square sellers to compare their business performance against industry standards. By analyzing anonymous data from similar businesses, sellers can identify areas where they excel or need improvement.

Instead of focusing on exact figures, Link My Books looks at percentage changes and trends, giving you a clear picture of how your business is performing relative to others. 

Cost of Goods Tracking

Tracking the cost of goods sold (COGS) is essential for understanding product profitability. Link My Books will take account of each of the products sold as part of your Square payouts. Then move their monetary value (landed cost) from your chosen inventory account to your chosen cost of goods sold account on the profit and loss statement.

By tracking COGS alongside revenue, you can make informed decisions about pricing, inventory management, and overall business strategy.

Accurate Tax Calculation

Managing taxes across different regions can be complex, especially for Square sellers who operate in multiple jurisdictions. Link My Books automates tax calculations, applying the correct rates based on where the sales occur. This automation ensures compliance with local tax laws, reducing the risk of errors and penalties.

Multi-Channel Support

Many Square sellers are active on multiple platforms, such as Shopify, eBay, or their own websites. Link My Books consolidates financial data from all these channels, providing a unified view of the business’s finances. This is crucial for sellers who need to manage inventory, track profitability, and generate comprehensive financial reports across different platforms.

Link My Books Pricing

We've kept our pricing as straightforward as possible for Square sellers. There are three plans available: Lite, Pro, and Premium. There is a slider for you to manually adjust your number of sales per month. The price of your plan will change to reflect this.

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Our Lite plans start from just £13/month or $17/month if you’re in the US, they include:

• Connect 1 sales channel
• 3 months of historical data

Our Pro plans start from just £23/month or $29/month if you’re in the US, they include:

• Connect up to 5 sales channels
• 12 months of historical data

Larger plans are available too with more orders and more channels.

All Link My Books yearly members can get a free two months of our software. 

Which Square Accounting Software is Best for You?

Choosing the best accounting software for your Square-based business depends on your specific needs, business size, and budget. Here’s a breakdown of the top options and how they might fit your situation:

• Xero with Link My Books: If your business requires robust financial reporting, multi-currency support, and detailed cost tracking, Xero with Link My Books is a top choice. It’s ideal for businesses that operate across multiple channels and need in-depth insights into profitability and tax compliance.
• QuickBooks Online with Link My Books: This software is perfect for businesses that value ease of use alongside powerful accounting features. It offers strong class tracking and reconciliation tools, making it suitable for businesses that need to manage detailed financial data across multiple sales channels.
• Zoho Books: Zoho Books is ideal for smaller businesses that need a cost-effective accounting solution with strong automation features. It’s particularly beneficial if you’re already using other Zoho products, as it integrates seamlessly across their ecosystem.
• Sage: If your business requires advanced financial reporting and inventory management, Sage is a great option. It’s well-suited for businesses that need to manage complex operations across multiple locations or channels.
• FreshBooks: FreshBooks is best for small businesses that prioritize simplicity and efficient invoicing. It’s user-friendly and offers essential accounting features without overwhelming you with complexity.
• Wave: If you’re just starting out or have a very small business, Wave offers essential accounting tools for free. It’s a good option if you’re on a tight budget and need basic financial management without the cost.

Getting Started with Link My Books

By integrating with top accounting software like Xero and QuickBooks Online, Link My Books ensures that every transaction is accurately recorded, taxes are applied correctly, and bank reconciliations are effortless. 

Ready to simplify your Square accounting? Start your free trial with Link My Books and discover how it can transform your bookkeeping process. 

By automating your financial tasks and providing valuable insights, Link My Books allows you to focus on what matters most - growing your business.

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