How To Manage Ecommerce Business Accounting & Bookkeeping? How To Do It With Accounting Software?

How do you actually manage your eCommerce business accounting and bookkeeping?

That’s one of the questions every seller asks sooner or later; usually after realizing how messy things can get once multiple sales channels, taxes, and payouts come into play.

In this guide, I’ll walk you through

1. What proper eCommerce accounting looks like,

2. How to do it manually or with software like Link My Books, and

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3. How it can make the process way easier and more accurate.

If you prefer to watch instead of read, I’ve got you covered.

Here’s the video version of this guide below.

Why Accounting Matters so Much for eCommerce Sellers

I get it.

Bookkeeping isn’t the most exciting part of selling online.

But it’s absolutely essential if you want to run your business like a real business.

Without proper accounting, you can’t really see your profits, track your taxes, or make smart decisions about growth.

When you sell across platforms like Amazon, Shopify, or Etsy, your finances quickly get complex.

You’ve got fees, refunds, advertising spend, and taxes that don’t show up neatly in one place.

That’s where most sellers start feeling overwhelmed.

Some even mix up revenue with profit or ignore their bookkeeping until tax season, which becomes a nightmare.

I actually wrote about that in another guide: Most Amazon Sellers Make This Bookkeeping Mistake.

So, if you’ve ever felt confused about how to manage your accounting properly, you’re not alone.

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The Manual Way: Doing Your Bookkeeping Yourself

Let’s start with the basics.

Yes, you can do your bookkeeping manually through spreadsheets, bank statements, and a lot of patience. 😮‍💨

Some sellers prefer it this way because they like control or their volume is still low.

You’ll record your income and expenses, categorize them, and reconcile your books each month.

It’s not a bad way to start.

In fact, it helps you understand your numbers.

But as soon as your sales grow across multiple channels, manual work starts eating up your time and leaves more room for mistakes.

That’s when most people begin looking into accounting software, something that connects your platforms automatically and keeps everything organized.

If you’re doing this manually, I also recommend checking my post on the best free bookkeeping resources.

It’ll help you get started the right way.

The Smarter Way: Using Accounting Software

Accounting software like QuickBooks Online or Xero is great because it automates a big part of your bookkeeping.

You can track expenses, connect bank accounts, and generate reports quickly.

But here’s the catch: when you sell through multiple eCommerce platforms, these tools can’t directly understand the detailed data from Amazon, Shopify, or eBay.

They don’t know what’s a refund, what’s a fee, or how to properly split taxes.

That’s why integration tools like Link My Books exist.

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How Link My Books Simplifies eCommerce Accounting

Link My Books bridges the gap between your sales channels and your accounting software.

It connects your Amazon, Shopify, eBay, Walmart, Etsy, TikTok Shop, Square, or WooCommerce account to QuickBooks Online or Xero, and automatically sends all your transactions over in a clean, accurate way.

No more manually exporting CSVs or trying to guess what those Amazon fees mean.

Everything syncs automatically and is broken down properly; sales, refunds, fees, taxes, and deposits.

It’s basically your eCommerce bookkeeping on autopilot.

Once you connect your accounts, you can even match Amazon payouts automatically to your bank deposits in Xero or QuickBooks.

It’s simple, saves hours each week, and ensures your numbers are always correct.

For example, if you want to understand how this integration looks in practice, check out my post about Amazon seller and QuickBooks integration.

It’ll give you a clearer picture of why this connection is so powerful.

How to Use Link My Books

For eCommerce Sellers

If you’re an eCommerce seller and want to see Link My Books in action, I’ve got a full tutorial with Daniel Little, the co-founder of Link My Books.

We go through everything step by step, from connecting your sales channels to syncing your data and reconciling your books.

You’ll see how to use it, what the setup looks like, and how to make your accounting easier and more accurate.

You can watch it here:

Or read the full article version here: Link My Books Tutorial and Review

Once you watch it, you’ll probably wonder why you didn’t automate this sooner.

For Accountants and Bookkeepers

If you’re an accountant or bookkeeper managing clients who sell online, Link My Books can save you tons of time while improving accuracy.

You’ll be able to onboard clients faster, reduce manual adjustments, and generate consistent reports for every platform.

Basically, it helps you scale without chaos.

I also made a full video for you, again with Daniel Little, showing how to use Link My Books for accounting practices.

Here’s that video:

And if you want to dive deeper into pricing for accountants, check out my detailed post: Link My Books Pricing For Accountants & Bookkeepers

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Real Benefits You’ll Notice

From my own experience using Link My Books, here are a few things that stand out:

1. It reduces human error; everything’s automated.

2. Your books stay consistent across all platforms.

3. You can actually understand where your profits are going.

4. It saves hours every week compared to manual bookkeeping.

And maybe most importantly, it gives you peace of mind.

You know your numbers are accurate and you’re not missing anything before tax time.

That’s something hard to put a price on.

A Quick Note Before You Jump In

Just a quick reminder: this isn’t financial advice.

Everyone’s business is different, so it’s best to talk to a certified accountant before making major financial decisions.

The good news is that the team at Link My Books can also connect you with trusted professionals who know eCommerce inside out.

And remember, you can test everything risk-free.

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Final Thoughts

Managing eCommerce accounting doesn’t have to be stressful.

Whether you’re a seller running multiple stores or a bookkeeper managing clients, having the right setup can save you hours every week and prevent costly mistakes.

You can always do it manually, especially if you’re just starting out.

But once things scale, tools like Link My Books become a lifesaver.

They make your accounting smooth, accurate, and automatic so you can focus more on growing your business.

Keep going, you’ve got this!

P.S. Explore our main Link My Books hub for tutorials, tools, discounts, and guides: https://vovaeven.com/link-my-books