May 4, 2024
9 min

WooCommerce Bookkeeping Software, Tips, FAQs, and More

Empower your e-commerce success with top WooCommerce Bookkeeping tips. Learn how to manage your finances like a pro and boost your business growth.
WooCommerce Bookkeeping Software, Tips, FAQs, and More
Table of contents

Are you constantly dreading the thought of putting your WooCommerce books in order? Or does the thought of preparing your taxes cause you anxiety and stress?

Or could it be that you’re not understanding your WooCommerce insights?

If you answer yes to these questions, then these WooCommerce bookkeeping tips are what you need!

Ready to dive in? Let’s get started.

Key Takeaways from this Post

Monitor Key Metrics: Track COGS, conversion rate, gross profit, cart abandonment rate, and ROI for a healthy store understanding.
Bookkeeping Practices: Manage cash flow, taxes, inventory, and employ an accounting solution for organized WooCommerce books.
Automation with Link My Books: Simplify bookkeeping with automated syncing of sales data, tax calculations, and streamlined reconciliation using Link My Books.
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TL;DR - What Do I Need to Know About WooCommerce Bookkeeping?

Don’t have time to read the entire post?

Here are the key takeaways:

  • Key WooCommerce Metrics: Monitor metrics like COGS, conversion rate, gross profit, cart abandonment rate, and ROI to understand the health of your store.
  • Bookkeeping Best Practices: Understand your cash flow, taxes, inventory stock, and choose an accounting solution to keep your WooCommerce books in order.
  • WooCommerce Bookkeeping on Auto-pilot: Link My Books is the best automation solution to link your WooCommerce bookkeeping with Xero (or QuickBooks). It saves you time, allows one-click account reconciliation, and provides a hassle-free tax calculation.

Buckle up as we expound on these (and other areas) related to WooCommerce bookkeeping.

Can You Sync WooCommerce Sales Data with QuickBooks or Xero?

Yes, you can sync WooCommerce sales data with QuickBooks or Xero using Link My Books.

Link My Books is the leading bookkeeping tool that helps you easily bring sales data — order information, customer data, and payment methods — to your Xero or QuickBooks.

That alone will help you reduce human error and save lots of time.

So, forget the hassle of manual data entry and set up Link My Books for free today.

A woman's hand adorned with a silver bracelet and ring typing on a laptop keyboard.

5 Woocommerce Bookkeeping Metrics

While there are over 24 e-commerce metrics, we’ll discuss the top 5 metrics driving WooCommerce success:

1. Cost of Goods Sold: Simply called the COGS, this metric helps you calculate the direct costs related to the production of your product.

To calculate the COGS, use this formula:

Cost of goods sold = Beginning inventory + Purchases – Ending inventory

A lower COGS indicates a high-profit margin, while a higher COGS shows your store is unsustainable and unable to make returns in the future.

2. Conversion Rate: This metric shows you the number of website visitors who converted to customers.

Here is the formula:

Conversion Rate = (Total Conversion/ Total Visitors) X 100

A high conversion rate means your marketing efforts effectively convert prospects to customers.

Overall, you should aim to increase this metric.

3. Gross Profit: As the name suggests, the gross profit shows whether your business has made a profit.

Check the formula below on how you should calculate it:

Gross profit = Gross revenue - Costs of goods sold

4. Cart Abandonment Rate: The cart abandonment rate is essential to show the number of customers who don’t complete the checkout process.

Use the formula below:

Cart Abandonment Rate = 1 - (Number of Completed Purchases / Number of Shopping Carts Created) x 100

When this metric is high, it could signal potential issues like a lengthy checkout process or additional costs. Aim to keep the cart abandonment rate low.

5. Return on Investment: The ROI metric helps you better understand your marketing and sales efforts and make informed decisions.

The formula to calculate the ROI is:

ROI = (Net Profit / Total Investment) x 100

When the ROI is high, it shows the net returns are greater than the total costs.

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How Does WooCommerce Streamline Bookkeeping?

Streamlining your bookkeeping helps you reduce manual data entry and stay on top of your finances.

Find out the two steps you should follow:

Build-in Tax and Reporting Dashboards

The native WooCommerce system automatically calculates your taxes by location and tax class. The system also sets up multiple tax rates easily.

WooCommerce also has a reporting dashboard to monitor gross sales, refunds, discounted orders, and more metrics.

On the flip side, WooCommerce doesn’t offer comprehensive analytics, and managing your taxes can be complex.


You can connect WooCommerce with your accounting tool, like Xero or QuickBooks, to generate detailed reports and manage your finances.

Then, you should use an automation solution like Link My Books, which integrates WooCommerce and Xero (or QuickBooks).

Link My Books simplifies your bookkeeping by breaking down each WooCommerce payout into fees, refunds, and sales taxes.

It also auto-calculates state and international taxes and creates summarized invoices that enable fast bank reconciliation. It automatically develops richer, better financial statements.

So, what are you waiting for?

Book a demo today of Link My Books today and you’ll be one step closer to streamlining your WooCommerce bookkeeping!

Top-down view of two warehouse workers with clipboards by a pallet of boxes.

WooCommerce Bookkeeping Best Practices 

It’s not enough to know how to streamline your bookkeeping. You must implement top practices to get your books in order.

Here are seven easy ways to do it:

1. Track Your Cash Flow

Poor cash flow management is among the leading causes of business failure. Therefore, you must stay aware of the money coming in (income) and cash going out of your WooCommerce store (expenses).

When monitoring your cash flow closely, you can ensure your business stays afloat, determine if your store is profiting or in debt, and resolve potential issues early.

2. Keep Up with Your Taxes

As a WooCommerce seller, you must track the sales, VAT, and GST tax amount you owe the government according to your tax jurisdiction. Note all upcoming taxes and the deadlines to avoid penalties and fines.

Also, account for all income and deductions.

3. Review Your Financial Reports Regularly

Routine financial checkups are vital to guide your decisions and ensure proper tax preparation. Compare and review reports like balance sheets, cash flow, and P&L statements.

Remember, up-to-date financial reports also help you ensure your transactions are accurately recorded.

4. Stay on Top of Your Inventory

With stock moving around and fluctuating cash flows, staying on top of your inventory is crucial for a smooth bookkeeping process.

So, perform periodic inventory audits to maintain accurate stock records, identify errors, and reduce stockouts. Besides, develop a system to easily track your stock levels and cash flow.

5. Keep Your Personal and Business Finances Separate

Mixing your personal and business finances is room for disaster. So, you need to separate these finances to make it easy to manage finances, reduce financial problems, and simplify your bookkeeping.

Open a bank account solely for your business. A dedicated business account makes tracking your business expenditures easy and allows for a smooth tax time.

6. Reconcile Your Accounts Regularly

Although there’s no hard rule to reconcile your accounts regularly, it does help to reconcile your bank statements once weekly or bimonthly. You can catch missed deposits and identify transaction discrepancies early on.

Ultimately, you can resolve issues quickly and stay on top of your finances.

7. Consider a Bookkeeping Automation Software

You shouldn’t have to manually track your inventory, calculate your taxes, or create financial reports.

Consider the best accounting solution that takes these repetitive tasks out of the way and automates your bookkeeping.

Link My Books can help you gain confidence in your books by automating tax calculations, allowing accurate inventory management, and creating detailed financial reports.

Try it now for seamless WooCommerce bookkeeping!

Best WooCommerce Bookkeeping Software

You’ve probably got a couple of accounting solutions, but which are the best? Check out our list of three great accounting tools and their top features.

1. Link My Books

Link My Books Homepage

Link My Books is the top accounting tool that helps you free up all your bookkeeping headaches. It seamlessly syncs WooCommerce data with Xero or QuickBooks.

Find out the top features below:

  • Dedicated 1:1 Onboarding Support: Link My Books can seamlessly connect with WooCommerce in under 15 minutes. Plus, you’ll get guided onboarding support to navigate the platform.
  • Supports Multiple Channels: This tool can connect up to 10 channels to provide a holistic view of all your channels' performance in one place.
  • Applies the Correct Tax Rates: Link My Books saves you the tax burden by automatically calculating the correct sales, VAT, or GST taxes.


  • Allows one-click reconciliation of your summary invoices to your bank deposits on Xero or QuickBooks.
  • Automatically syncs all your customer’s data, sales, and order details, reducing the need for manual data entry.
  • Supports multiple currencies and accurately creates COGS reports.

2. Synder

Synder Homepage

Synder is a bookkeeping tool that helps connect your store to your accounting tool.

Let’s explore Synder's top features:

  • Accurate Financial Data: Synder connects WooCommerce with your accounting tool to ensure all your data is synced, leading to organized and accurate records.
  • Streamline Invoicing: This tool allows you to create, send, and track invoices.


  • Allows easy bank reconciliation
  • Generate reports to provide insights into your financial performance

Potential Cons

  • Has a complex interface, and the learning curve can be challenging
  • Lacks the ability to import invoices

3. Xero

Xero Homepage

Xero is another accounting tool that syncs data automatically from your WooCommerce store and reduces manual data entry.

Here are its key features:

  • Ease in Syncing Data: Xero connects with WooCommerce to seamlessly sync product, shipping, and tax information for each order.
  • Generating Invoices: Xero can automatically create invoices for your WooCommerce orders.


  • Xero offers unlimited users, but on its lowest tier, there’s a limit to the invoices you can send.
  • Ideal for e-commerce sellers since it’s easy to use

Potential Cons

  • Sometimes, there can be errors in tax calculations and inaccurate bank reconciliation.

The right accounting tool will help you create invoices, organize financial data, and reconcile accounts.

Frequently Asked Questions (FAQs)

Check out the next section to discover the answers to the common questions about WooCommerce bookkeeping.

How Can I Handle Taxes and VAT in WooCommerce Bookkeeping?

The best way to handle taxes and VAT is by integrating your WooCommerce with Link My Books.

Once you’ve set the right VAT group (standard, reduced, or zero) for your products, Link My Books will apply the correct tax rates to products.

Also, this tool auto-calculates the sales and GST taxes you owe on each transaction.

With Link My Books, you’ll not have to overpay taxes again.

What Challenges Do WooCommerce Store Owners Face in Bookkeeping?

Here are the common bookkeeping challenges for WooCommerce sellers.

  • Recording and calculating sales, VAT, and GST taxes can be complex, as well as keeping current with state and international tax laws.
  • Tracking and managing inventory stock levels can be challenging. Errors can arise, leading to overselling, lost sales, and stockouts.
  • There are complexities when dealing with high sales volumes and multiple currencies, making it difficult to track your financials.

How Do I Automate Sales Tax Compliance in WooCommerce?

You can automate your WooCommerce sales tax compliance using the Link My Books accounting solution.

With each WooCommerce payout, Link My Books automatically spits it into sales, fees, and refunds. It also applies the correct tax rates on each transaction. Another huge plus is that Link My Books stays current on tax law changes.


We hope this guide helps you to handle all your bookkeeping functions easily.

As we wrap up, remember to monitor your cash flow, track your taxes, and review your financial statements frequently. Also, don’t forget to monitor your inventory closely, create a dedicated business account, and regularly reconcile accounts.

However, you don’t have to feel overwhelmed when you can automate all these bookkeeping functions using the best accounting tool — Link My Books.

The platform auto-categorizes transactions, auto-calculates taxes, and allows one-click bank reconciliations. It also generates detailed financial reports (and analytics) to help you make better decisions.

Ready to roll? Book a demo today and explore how to use Link My Books for your online store.

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