Top 8 Bookkeeping Services for Ecommerce Entrepreneurs

“When I started my first local business I didn’t know anything about taxes, bookkeeping, and accounting (and I still don’t). But my first bookkeeper was so BAD. Basically he wouldn’t pick up my calls for days, hardly responding to my messages and emails. And when sending some important bills or pension and health care related docs, he would just send an attachment through Email with a bill. I didn’t know what it was and after some time got in big big trouble and had to pay 1000s in fines and they couldn’t even tell me why I was fined.“

A true story from a Reddit user.

If you’re an ecommerce entrepreneur, chances are you’ve experienced some version of this frustration.

But, here’s the silver lining: bookkeeping has come a long way. 

Now, there are bookkeeping services designed specifically for ecommerce businesses — ones that actually care about your finances.

And this blog..is just for you, the hustling ecommerce entrepreneur who’s been burned by unresponsive bookkeepers or left drowning in financial confusion.

Here’s what we’ll cover:

👉 What to look for in a bookkeeping service (key features): Because not all services bring their A-game

👉 Limitations: Get a clear understanding of potential drawbacks so you can make informed decisions and avoid surprises

👉 Pricing: The all-important factor. You should know what’s coming before it hits your wallet.

Ready to declutter your finances? Dive right in.

And if you still have questions about taxes, numbers, or anything bookkeeping-related, reach out to our experts anytime. 

Just book a free demo and you’ll have all your answers. Promise!

How to Choose the Best Bookkeeping Service for Your Ecommerce Business

Picking the right bookkeeping service doesn’t have to be a tiring chore. Have an outline of what you actually need. 

Take a look at your core bookkeeping concerns. 

After that, start your research and do your ground work. Compare, read reviews and see what your competitors are using. 

Don’t settle for less than someone who truly gets your business.

Here’s how you can avoid the bad apples and find the perfect bookkeeping service.

1. Define What You Need

Start by figuring out your bookkeeping blockers. Do you need someone to cover the basics, like tracking income and expenses? 

Or are you after something a little more specialized — sales tax compliance, inventory tracking, or reconciling across multiple ecommerce platforms?

Here’s your first red flag: If a service doesn’t integrate with ecommerce platforms like Shopify, Amazon, or Etsy, it’s probably not the right fit for you.

2. Look for Ecommerce-Specific Expertise

Not every bookkeeper understands the world of ecommerce. 

So many developments occur each day in the ecommerce sector. 

Ecommerce bookkeeping is more than just logging transactions. It’s about managing returns, juggling multiple revenue streams, and keeping track of inventory across platforms and warehouses.

You wouldn’t hire a generalist to solve a specialized problem, right? 

You need someone who’s been there, done that, and understands the rollercoaster of running an ecommerce business.

So, find a bookkeeping partner who understands the ins and outs of the ecommerce industry.

3. Prioritize Clear and Responsive Communication

Nothing’s worse than feeling left in the dark when you need answers. A good bookkeeper should:

✅ Respond quickly to your questions.

✅ Explain things in plain, everyday language — not accounting jargon that leaves you even more confused.

Here’s doola’s tip: send them a question during your research phase. If their reply feels slow or overly complicated, it’s a sign of how they might handle your business later.

4. Read Reviews — and Pay Attention to the Details

This step is non-negotiable. Reviews give you an inside look at what it’s like to work with a service.

Look for feedback from other ecommerce entrepreneurs who’ve used their services.

Are people thrilled about how smooth tax season was, or are they ranting about missed deadlines and surprise fees? 

Keep an eye out for patterns. Pay attention to recurring themes in the reviews — both good and bad.

Better yet, ask fellow business owners for referrals. A trusted recommendation can save you from a world of trouble.

Check these trusted sources for feedback from other ecommerce entrepreneurs: ✅ Google Reviews: Search for the service name and read reviews from verified users. Look for consistent themes, like responsiveness, accuracy, or problem-solving. ✅ Trustpilot: A go-to site for honest, detailed customer reviews. Many bookkeeping services have profiles here where users share their experiences. ✅ Facebook Groups and Communities: Join ecommerce or small business groups (like Ecommerce Entrepreneurs or Amazon Sellers Network) and ask for recommendations. Real-life feedback from your peers can be incredibly helpful. ✅ Reddit: Check subreddits like r/Ecommerce or r/SmallBusiness. Search for the service name or post your own question asking for feedback. Redditors are often brutally honest. ✅ Industry-Specific Forums: Look for forums dedicated to ecommerce platforms you use, like Shopify Community or Amazon Seller Forums. These often have threads discussing bookkeeping services. ✅ G2 and Capterra: Both are excellent platforms for finding in-depth reviews of business tools and services, including bookkeeping solutions. For example, check how doola’s bookkeeping users have reviewed our bookkeeping services. Hunt for similar reviews!

5. Understand Their Pricing

Budget matters, so make sure you fully understand their pricing model. Do they charge a flat monthly fee, or is it an hourly rate? 

Are there hidden costs, like additional charges for filing taxes or reconciling accounts?

If you find yourself squinting at a long list of confusing fees, that’s your cue to move on.

6. Take Advantage of Free Trials or Demos

Many bookkeeping services offer free trials or consultations. 

Use this opportunity to test the waters. Is their platform user-friendly? Do they ask relevant questions about your business? Do they explain their services clearly?

This is your “trial run” to see if they’re as good as they claim to be.

If you’re still feeling unsure, let us help! Book a free demo, explore your options and get your questions answered. 

Top 8 Bookkeeping Services for Ecommerce Businesses

Managing bookkeeping for an ecommerce business requires precision, time, and expertise. 

Choosing the right bookkeeping service can help you simplify this process, ensure compliance, and free up your time to focus on growth. 

Here’s a detailed look at the top 8 bookkeeping services tailored for ecommerce businesses.

1. doola Bookkeeping

Overview: doola offers an all-in-one digital accounting and bookkeeping solution tailored for entrepreneurs and small businesses, focusing on real-time financial management and tax compliance.

Key Features:

✅ Seamless Integration: Connects with various financial accounts for streamlined management.

✅ Expert Support: Provides access to a dedicated bookkeeper supported by a team of specialists.

✅ Interactive Reports: Delivers monthly and year-end financial statements that are easy to analyze.

✅ Tax Compliance: Manages income tax filings to ensure compliance.

✅ Real-Time Assistance: Allows direct messaging with your bookkeeping team within your account.

✅ Consultation Calls: Offers free scheduling of calls with your bookkeeping team for guidance.

Pricing:

💲 Bookkeeping Software: $25 per month.

💲 Dedicated Bookkeeping: $167 per month.

💲 Dedicated Tax Filing: $125 per month.

💲 All-in-One Accounting: $249 per month.

Read more.

2. QuickBooks Live

Overview: QuickBooks Live pairs QuickBooks Online software with certified bookkeepers to assist ecommerce businesses in maintaining their books.

Key Features:

✅ Real-Time Tracking: Automates categorization of transactions.

✅ Monthly Reviews: Bookkeepers review and close books each month.

✅ Customization: Offers tailored invoicing and financial reporting.

✅ Ecommerce Syncing: Integrates with platforms like Shopify and Amazon.

Pricing:

💲Base Plan: Plans range from $30 to $220 per month.

Limitations:

❌ Integration Limitations: While it integrates with major platforms, some niche ecommerce tools may not be supported.

3. Xendoo

Overview: Xendoo provides flat-rate bookkeeping and tax solutions, focusing on delivering timely financial insights for small businesses.

Key Features:

✅ Weekly Bookkeeping Updates: Ensures up-to-date financial information.

✅ Tax Compliance: Includes tax preparation and filing services.

✅ Ecommerce Integrations: Supports platforms like Shopify, WooCommerce, and Amazon.

✅ CPA Support: Access to certified professionals for complex financial needs.

Pricing:

💲 Starter Plan: $295 per month.

💲 Growth Plan: Custom pricing for larger businesses.

Limitations:

❌ Service Scope: May not offer highly specialized services required by some ecommerce businesses.

❌ Pricing Structure: Flat-rate pricing might not be cost-effective for businesses with minimal transactions.

4. A2X

Overview: A2X is a bookkeeping automation tool designed for ecommerce sellers, facilitating accurate financial data transfer between ecommerce platforms and accounting software.

Key Features:

✅ Automated Sales Categorization: Organizes sales, fees, and taxes automatically.

✅ Multi-Currency Support: Handles international transactions efficiently.

✅ Seamless Integration: Works with Shopify, Amazon, eBay, and Etsy.

✅ Accounting Software Sync: Connects with QuickBooks Online and Xero.

Pricing:

💲 Starter Plan: $19 per month.

💲 Professional Plan: $69 per month.

Limitations:

❌ Support Limitations: Customer support may be limited compared to full-service bookkeeping providers.

5. Pilot

Overview: Pilot offers full-service bookkeeping tailored for startups and ecommerce businesses, focusing on accrual-based accounting.

Key Features:

✅ Accrual-Based Accounting: Ideal for more complex financial needs.

✅ Dedicated Bookkeeper: Assigned to handle reconciliations and financial oversight.

✅ Ecommerce Expertise: Integrates seamlessly with Shopify, Stripe, and Amazon.

✅ Tax-Ready Financials: Prepares detailed year-end statements.

Pricing:

💲 Starter Plan: $349 per month.

💲 Growth Plan: Custom pricing based on business size.

Limitations:

❌ High Cost: May be out of budget for smaller businesses.

❌ Focused on Startups: Service offerings may not suit larger-scale operations.

6. Wave

Overview: Wave provides free accounting software with optional paid bookkeeping and payroll services, making it great for startups and small-scale ecommerce businesses.

Key Features:

✅ Free Expense Tracking: Tracks income and expenses automatically.

✅ Invoicing: Create professional invoices and accept online payments.

✅ Bookkeeping Add-On: Paid bookkeeping support available for more complex needs.

✅ Payroll Services: Optional add-on for growing businesses.

Pricing:

💲 Basic Software: Free.

💲 Pro Plan: $16 per month.

Limitations:

❌ Scalability Issues: Limited features for larger ecommerce businesses.

❌ Basic Functionality: May not suit businesses requiring advanced reporting or integrations.

7. Bookkeeper360

Overview: Bookkeeper360 provides a wide range of financial services, including bookkeeping, payroll, and CFO advisory, catering to growing ecommerce businesses.

Key Features:

✅ Customizable Reports: Tailor reports to suit your specific needs.

✅ Real-Time Tracking: Automates expense and income categorization.

✅ Payroll Services: Manage employee payments seamlessly.

✅ Ecommerce Integrations: Syncs with QuickBooks Online, Xero, and ecommerce platforms.

Pricing:

💲 Starter Plan: $399 per month.

💲 Premium Plan: Custom pricing based on additional services.

Limitations:

❌ U.S.-Centric: Limited support for international businesses.

8. Bench

Overview: Just like doola, Bench pairs intuitive bookkeeping software with human bookkeepers to deliver monthly reports and keep your finances on track.

Key Features:

✅ Dedicated Bookkeeper: Assigned to reconcile accounts and organize financials.

✅ Monthly Financial Statements: Includes income statements and balance sheets.

✅ Tax Season Support: Provides year-end financials to simplify tax filing.

✅ Ecommerce Integrations: Syncs with Shopify, Amazon, Stripe, and PayPal.

Pricing:

💲 Basic Bookkeeping Plan: $239 per month.

💲 Premium Plan: Custom pricing for tax-inclusive services.

Limitations:

❌ Cash-Basis Accounting Only: Businesses needing accrual accounting may not find this suitable.

How Can an Online Bookkeeping Service Help Your Ecommerce Business?

We know, as an ecommerce business owner, your days are a whirlwind of running campaigns, keeping customers happy, and juggling supplier relationships. 

And adding bookkeeping to that list? Hard pass

Here are a few tasks a bookkeeping service can take off your plate and keep you calm and sorted.

1. Recording and Categorizing Transactions

Let’s say, you sell on Shopify and Etsy, and you are probably processing dozens (or even hundreds) of transactions daily. 

Now, keeping track of every sale, refund, and shipping fee feels can be an exhausting task. Don’t you agree?

A bookkeeping service logs each transaction whether it’s revenue, shipping costs, or advertising expenses and categorizes them correctly in real time, so your records are always up-to-date.

2. Managing Sales Tax Compliance

If you’re selling across states — or internationally — you likely owe sales tax in multiple jurisdictions. 

Keeping up with different tax rates and filing deadlines is daunting. A bookkeeping service tracks your sales tax obligations and ensures timely payments. 

For example, if your Amazon FBA inventory creates a nexus in a new state, a bookkeeping advisor from a bookkeeping service can identify it and prepare the necessary filings, avoiding penalties.

3. Reconciling Accounts

Your payment gateways (like PayPal or Stripe), ecommerce platforms, and business bank accounts must work together seamlessly to provide accurate financial data. 

This means that every transaction recorded in your payment gateways and ecommerce platforms should match the deposits and withdrawals in your bank account. 

For example, let’s say your Shopify payouts don’t match the amount deposited in your bank account. This could be due to processing fees, refunds, or a missed transaction. 

A bookkeeping service identifies and resolves these discrepancies, ensuring your financial records are accurate and saving you the headache of doing it yourself.

4. Tracking Inventory Costs

Consider this instance where you’ve ordered a new shipment of products from a supplier overseas. 

But between shipping fees, customs charges, and supplier invoices, you’re not sure how much each item is actually costing you.

A bookkeeping service tracks every expense tied to inventory — purchase orders, shipping, and even storage costs. So you can calculate your cost of goods sold (COGS) and make informed pricing decisions.

5. Preparing Financial Reports

Understanding where your business stands financially is an important aspect of ecommerce bookkeeping. But as we know, creating intricate financial reports takes time and expertise.

A bookkeeping service prepares essential reports, such as profit and loss statements, balance sheets, and cash flow summaries. They can even break down which products are generating the highest margins, helping you make smarter inventory decisions.

6. Preparing for Tax Season

We probably don’t need to spell this out for you. Tax season is always overwhelming when your books are a mess.

But a good bookkeeping service can take that chaos off your plate.

A reliable bookkeeping service ensures all your financial records are accurate, neatly categorized, and ready to hand over to your accountant. 

5. Handling Vendor Payments

A bookkeeping service also organizes and schedules payments, ensuring all vendor invoices are paid on time and recorded accurately.

No more late payments or stressed-out suppliers.

Tips for Business Owners to Simplify LLC Bookkeeping

So, you’ve learned how a bookkeeping service can take the hassle out of your finances, in your ecommerce business. Want to take a step further? 

Here are a few DIY tips for business owners like you who are looking to streamline and simplify their LLC bookkeeping.

1. Separate Personal and Business Finances

Open a dedicated business bank account for your LLC. This keeps personal and business expenses separate, making your bookkeeping cleaner and your records audit-proof.

2. Choose Simple Accounting Software

Invest in easy-to-use accounting software or platforms like doola Bookkeeping, QuickBooks, Wave, or FreshBooks. These tools automate tasks like tracking expenses, sending invoices, and generating reports, freeing up your time for more important things.

3. Create a Weekly Bookkeeping Routine

Set aside 30 minutes each week to review your transactions, categorize expenses, and update your records. Doing this consistently keeps your bookkeeping manageable and prevents a last-minute run during tax time.

4. Save and Organize Receipts

Use a receipt tracking app like Expensify or even your phone’s camera to snap and store receipts digitally. Organize them into folders (e.g., meals, travel, office supplies) so they’re easy to find when you need them.

5. Reconcile Your Bank Statements Monthly

 At the end of each month, compare your bank statements with your recorded transactions. This helps catch mistakes, duplicate charges, or missing income before they become major issues.

6. Create an End-of-Month Checklist

Develop a simple monthly checklist that includes tasks like reconciling accounts, reviewing expenses, and categorizing transactions. This ensures nothing gets overlooked.

doola’s Tip: Take 5 Minutes to Meditate and Journal Your Financial To-Do List

It’s hard to focus when your brain feels like a browser with too many tabs open. And that happens once you dive into bookkeeping.

Take five minutes to breathe, meditate, and RESET. Then grab a pen and journal your financial to-do list.

Write everything down — bucketed into sections like “Track Expenses,” “Reconcile Accounts,” or “Prepare Tax Savings” in that old school way:)

 It’s a small step that works wonders.

Why Does This Work So Well for Entrepreneurs?

Taking a moment to calm your mind and jotting down your priorities creates a mental connection that digital tools just don’t replicate.

It’s a mindset shift that ensures you’re intentional and in control of your thoughts, rather than reactive and scattered.

Pair your journal session with a cup of tea or coffee to make it feel like a moment of self-care, not just another chore. You’ll be surprised how much clearer your financial tasks feel afterward!

Ready to Take Charge of Your Finances? Let doola Bookkeeping Help You

Alright, let’s wrap this up. 

Hopefully, you’ve got a better handle on how to approach bookkeeping — whether you’re DIYing it or partnering with one of these powerful bookkeeping services.

Just remember this one thing: your bookkeeping needs are as unique as your business. There’s no one-size-fits-all solution.

So take your time, trust your gut, and choose the tool or service that works best with your current setup, your tools, and, most importantly, your team.

Got questions? We’re all ears. 

Book a demo with our bookkeeping team, and they’ll help you figure out the best way to kick off this new chapter.