Link My Books Tutorial for Accountants & Bookkeepers

Link My Books helps accountants and bookkeepers automate e-commerce bookkeeping by connecting sales channels like Amazon, Ebay, Shopify, and Etsy to Xero or QuickBooks.

It turns messy payout data into clean, reconciled entries with correct tax treatment, saving hours every month and making multi-channel clients easier to manage.

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Why e-commerce bookkeeping feels harder than it should

If you’ve worked with e-commerce clients, you already know the problem.

Multiple sales channels.

Different payout schedules.

Fees, refunds, VAT rules that change by country.

And then you’re expected to reconcile all of that cleanly.

Most accountants try to solve this with spreadsheets.

It works… until it doesn’t.

Numbers don’t fully match.

Tax treatment becomes uncertain.

And every month feels like starting from scratch.

That’s exactly where tools like Link My Books come in.

Not to “assist” your process, but to replace the manual parts entirely.

What Link My Books actually does (in plain terms)

Link My Books connects your client’s sales channels directly to their accounting system.

But the real value is not the connection.

It’s what happens after.

It:

1. Breaks down each payout into real transactions

2. Applies correct tax rates automatically

3. Maps everything into the right accounts

4. Posts clean summaries into Xero or QuickBooks

5. Matches deposits during reconciliation

So instead of working from raw reports, you work from structured, verified data.

If you want a deeper understanding, this guide on bookkeeping and accounting for e-commerce sellers explains how Link My Books does it all.

Who this guide is really for

This isn’t for beginners learning bookkeeping.

It’s for:

1. Accountants handling Amazon, Shopify, Etsy, or eBay sellers

2. Bookkeepers dealing with multi-channel clients

3. Firms looking to scale without hiring more staff

4. Professionals who want to move into advisory, not just compliance

If that’s you, this guide shows exactly how to set up and use Link My Books properly.

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Step 1: Adding your first client (and getting it right)

The process starts simple, but this step matters more than most people realize.

You create a client account, add a name, and optionally assign a reference number.

That reference becomes useful later when managing multiple clients.

Next, you select the client’s sales channels.

Link My Books supports:

1. Marketplaces like Amazon, eBay, Etsy, Walmart, TikTok Shop

2. Platforms like Shopify, WooCommerce, and Square

Once selected, you decide how billing works.

Most firms choose to manage subscriptions themselves.

It keeps everything centralized and easier to control, especially when bundling services.

Then comes the connection phase.

You link Xero or QuickBooks, invite the client, and they connect their sales channels through a secure link.

No passwords to manage. No confusion.

Once connected, you’re ready for setup.

Step 2: The setup wizard (where accuracy is decided)

This is where your system either becomes clean… or messy long-term.

The setup wizard focuses on two things:

1. Account mapping

2. Tax configuration

Choosing your chart of accounts

You have three options:

You can use the default setup if the client is new or messy.

It creates a clean e-commerce structure automatically.

You can use a custom chart if you already have a system in place.

Or you can copy from another client.

This is where things get efficient.

Once you build a strong structure once, you reuse it across your entire client base.

That consistency alone saves hours later.

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Step 3: Setting up VAT and tax correctly

This is where many accountants hesitate and rightly so.

Tax rules vary by region.

Link My Books adapts based on the client’s location.

For UK clients, VAT setup includes:

1. Standard-rated sales

2. Reduced rates

3. Zero-rated categories

4. Amazon-handled VAT

5. International sales

The system suggests tax rates based on your accounting software, but you still review and confirm them.

If you need clarity on VAT differences across Europe, this secret map of VAT rates in Europe is worth checking.

Once confirmed, the system is ready to process real data.

Step 4: What actually happens after setup

This is where the shift happens.

Instead of working with spreadsheets, you now work with structured payouts.

Every payout is broken down into:

1. Individual orders

2. Shipping origin and destination

3. Product type

4. Fees and adjustments

Then it’s all mapped, taxed, and posted as a clean invoice into Xero or QuickBooks.

The bank deposit matches the invoice automatically.

Reconciliation becomes a few clicks.

If you’ve been doing this manually, you’ll notice the difference immediately.

For a deeper look at automation benefits, this guide on automating your bookkeeping and accounting as an eCommerce seller explains the impact well.

Step 5: Advanced control (when basic setup isn’t enough)

Once you’re comfortable, you can go deeper.

You can:

1. Assign tracking codes per marketplace

2. Split Amazon sales by fulfillment method

3. Separate shipping income from product revenue

4. Handle subscription fees differently from transaction fees

This is where Link My Books stops being a tool and becomes a system tailored to your workflow.

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Step 6: Financial analytics that actually matter

Most tools stop at bookkeeping.

This one doesn’t.

Inside Link My Books, you can analyze:

1. Sales trends

2. Refund ratios

3. Profit and margins

4. Tax liabilities

5. ROI

And more importantly, you can compare periods.

If refund rates increase, you spot it early.

If profit drops, you investigate faster.

This is where your role shifts.

You’re no longer just reporting numbers.

You’re explaining them.

If you want to understand why this matters, read why accurate accounting is important for your business.

Step 7: Seeing performance by channel (where real insights happen)

This is where things get interesting.

Instead of one combined P&L, you can break it down by channels.

This allows you to quickly see what’s actually driving profit.

Sometimes, a client spends most of their effort on one platform, but another platform generates most of the revenue.

That’s the kind of insight clients pay for.

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Step 8: VAT audit (for confidence and corrections)

The VAT Audit tool is simple but powerful.

It shows how revenue and expenses are distributed across tax rates.

This helps you:

1. Validate VAT returns

2. Check consistency

3. Spot discrepancies

If something looks off, you catch it early.

In some cases, it even reveals overpaid VAT – something clients definitely care about.

Step 9: Industry benchmarking (where you become valuable)

This is the shift from bookkeeping to advisory.

You can compare your client’s metrics against industry averages.

For example:

1. If their fee ratio is higher than competitors

2. If margins are lower than expected

You now have a clear conversation.

No guesses and no opinions, but data.

This is where you move from “doing accounts” to actually helping clients grow.

Step 10: Pricing and scaling your firm

Link My Books becomes more valuable as you grow.

Instead of charging per task, many firms bundle:

1. Bookkeeping

2. Software

3. Advisory

Into one monthly fee.

If you want a breakdown, check out my latest guide on Link My Books pricing for accountants and bookkeepers.

The key idea is simple:

More clients doesn’t mean more manual work anymore.

Start using Link My Books (and test it properly)

If you’re serious about improving your workflow, don’t overthink it.

Start with one client.

Test the full flow:

1. Setup

2. Mapping

3. First payout

4. Reconciliation

That’s enough to see the difference.

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You can also explore this full free trial of Link My Books guide if you want a walkthrough before signing up.

Final thought: what this actually changes for you

Link My Books isn’t just about saving time.

It’s about:

1. Reducing errors

2. Handling more clients without burnout

3. Delivering better insights

4. Charging for value, not hours

It's is a practical system for accountants and bookkeepers who want to manage e-commerce clients with less friction and more confidence.

So if your firm works with e-commerce sellers and you want a workflow that is more scalable, more accurate, and easier to build around, Link My Books is well worth a close look.

Claim Free Trial of Link My Books + Coupon Code VOVA20 To Get 50% OFF for 3 Months

If you're still confused or have specific questions before getting started, read my guide on Link My Books FAQ for accountants and bookkeepers.

It covers most edge cases.

Until next time.

Vova :)

P.S. - I recently published a guide explaining whether WooCommerce integrates with Xero, how the connection works, and how to automate your accounting and bookkeeping setup, read here: Does WooCommerce Integrate With Xero? Best Accounting & Bookkeeping Integration Software Tool & App