Best Accounting & Bookkeeping Software for Online Retail

The quick answer

What is the best accounting and bookkeeping software for online retail?

For an online retailer using Xero or QuickBooks Online, Link My Books is a strong specialist option. It connects marketplaces and stores to your bookkeeping system, organizes sales, refunds, fees and taxes into settlement summaries, and helps match those summaries with bank deposits. It is especially useful for Amazon, Shopify and multichannel sellers, as well as accountants managing e-commerce clients. The best fit still depends on your accounting platform, sales channels and tax requirements.

Why is bookkeeping for an online store so complicated?

The challenge is not just recording orders. It is connecting the orders to money received while keeping every deduction in the correct category. Amazon, for example, can combine many sales and adjustments into a single settlement. Shopify may involve several payment gateways, while a seller using Etsy and eBay must account for two more sets of fees and payout dates.

Consider a simplified example: your store records $10,000 in sales, $500 in refunds and $800 in platform fees. The resulting transfer could be $8,700 before any other adjustments. Recording only the deposit as sales would hide the original revenue, returns and expenses. Those details matter when you measure margins or prepare accounts.

Manual spreadsheets can work at a small scale, but the more channels and transactions you add, the more opportunities there are for missed fees, duplicated entries and mismatched deposits. A good integration reduces that repetitive work while preserving enough detail to investigate an unusual number.

How does Link My Books work with Xero and QuickBooks?

Link My Books acts as a bridge between a selling platform and your accounting records. After you authorize the connections and configure the account and tax mappings, it imports settlement information and organizes the financial activity within those payouts.

An important distinction: the software does not have to create a separate accounting entry for every customer order. Its official data-posting explanation says Xero receives an invoice for each settlement, while QuickBooks Online receives a sales journal. The entries use your chosen accounts and tax rates, with an audit report available for reference.

Once the mappings are correct, much of this can run automatically. You should still check the first settlements carefully: a repeated mistake in the original configuration can become a repeated mistake in your books.

Which online retail platforms integrate with Link My Books?

The current Link My Books integration and pricing page lists eight sales channels. The table covers the practical differences worth checking before connecting an account.

Not every marketplace is supported in every country. If you are selling through Walmart outside the US or TikTok Shop outside the US and UK, verify your specific account before purchasing.

Is Link My Books for sellers or accountants?

Both. For a seller, the main benefit is a clearer picture of revenue and expenses without rebuilding the numbers manually each month. This can be particularly helpful when you operate more than one storefront or start selling in additional marketplaces.

For accountants and bookkeepers, the advantage is repeatability. A practice can use consistent mappings and settlement workflows for different e-commerce clients, spending less time importing reports and more time reviewing results. Additional user access also makes collaboration easier.

Neither group should expect software to make accounting judgments on its own. Someone still needs to review the chart of accounts, choose appropriate tax treatment, and confirm that the reports reflect how the business really operates.

How do you set up Link My Books?

I would start with one sales channel and one settlement. That gives you a complete test without changing every part of your bookkeeping at once. The provider's setup guide outlines four broad stages; here is the more practical checklist I recommend.

1. Create your account. Sign up for the trial and select whether you are a business owner or accounting professional.
2. Connect a sales channel. Authorize Amazon, Shopify or another supported store using the relevant platform connection.
3. Connect your bookkeeping system. Choose Xero or QuickBooks Online and confirm that the correct company is selected.
4. Review account mappings. Decide where sales, returns, platform fees and other settlement components should appear.
5. Configure taxes. Work through the tax wizard and have your accountant verify unfamiliar rules.
6. Check the first settlement. Compare it with the marketplace report before posting it into the books.
7. Reconcile the deposit. Match the actual bank transaction, investigate differences, and only then enable your preferred automation settings.

The first review is the important one. If Amazon charges a fee or Shopify reports a refund, you want to see it in the right account rather than discover months later that the figures were categorized incorrectly.

You can use this compatibility guide before connecting your accounting software. QuickBooks Desktop and QuickBooks Self-Employed are not supported; Xero's entry-level invoice limits and any multicurrency requirements also deserve attention.

Does Link My Books handle VAT, GST and sales tax?

It provides built-in support for categorizing taxes in e-commerce settlement data, including VAT, GST and sales-tax scenarios. Its guided tax setup can help apply the rates and mappings you choose, including different product groups where supported. That matters when a marketplace collects tax, when you sell across borders or when your products have different tax treatments.

However, tax recording and tax compliance are not the same thing. The software cannot decide where your business should register, guarantee that every rate is appropriate or replace professional advice on returns. Those responsibilities depend on your business structure, products and jurisdictions.

My suggestion is to treat automation as an accurate recording process that still needs correct inputs. Review the first tax reports with a qualified professional, particularly if you sell internationally or have a mix of taxable and exempt products.

How much does Link My Books cost?

Link My Books prices subscriptions according to factors such as your average monthly order volume, connected sales channels and historical data requirements. Rather than quoting a rate that might not apply to your business, I recommend entering your actual numbers into the official pricing calculator.

The standard trial currently lasts 14 days, requires no credit card and imports the most recent 90 days of settlements. Paid plans may include a longer lookback period. Free onboarding is listed as part of the service, so use it to ask about your particular platform, tax mapping and first bank reconciliation.

If you plan to keep the subscription, compare the regular recurring price as well as the promotional price. Also check how the service counts sales channels and whether growth in order volume could move you to a higher tier.

Free Link My Books tutorials for sellers and bookkeepers

I recorded two longer walkthroughs with Daniel Little, the co-founder of Link My Books. Choose the one that matches your role. Both go beyond this introduction and show how the software fits an actual working process.

What should you check before relying on bookkeeping automation?

Link My Books can remove much of the work of gathering and posting settlement data, but it is not a replacement for Xero or QuickBooks as your main accounting ledger. You may still need separate systems for invoicing outside your store, payroll, inventory planning, tax filing or deeper product-level profitability analysis.

I would also review the reports whenever something changes: a new marketplace, payment gateway, tax registration, fee structure or refund policy. An automated system is most valuable when you understand what it is doing and can recognize when the numbers no longer look right.

A good first-month test is simple. Confirm that every payout matches, key fees have the right classification and your accountant is comfortable with the tax setup. Once those checks pass, the time savings become much easier to trust.

Frequently asked questions about Link My Books