Find Accountants for Ecommerce – Top 11 Services to Consider

E-commerce businesses need more than just great products; they need accurate financial management to stay profitable.

With global ecommerce sales expected to reach $8.09 trillion by the year 2028, having the right accountant can make all the difference in optimizing cash flow, reducing tax burdens, and ensuring compliance.

But with so many options, how do you choose the best one? Whether you’re a Shopify seller, an Amazon FBA business, or running a multichannel store, you need an accountant who understands platform fees, inventory management, and sales tax complexities.

In this blog, we’ll discuss ten accounting services that will help you run your e-commerce business smoothly.

TL;DR – Best Accountants for Ecommerce

Here is a quick and curated list of the ten best accountants for your ecommerce business:

1. EcomBalance
2. inDinero
3. 1-800Accountant
4. Paro
5. Bench Accounting
6. Pilot
7. Merritt Bookkeeping
8. Bookkeeper.com
9. BKE (formerly Bookkeeper 360)
10. Xendoo
11. Justworks

While these accountants are great options, you need to find a service that truly understands the unique challenges of ecommerce, which will make all the difference.

That’s where EcomBalance comes in! We offer tailored ecommerce bookkeeping services designed specifically for ecommerce businesses.

We offer accurate bookkeeping, seamless platform integration, and expert financial reporting to keep you on top of your numbers.

Schedule a consultation today!

Why Ecommerce Businesses Need Specialized Accounting

Ecommerce businesses operate differently than other offline businesses; they require specialized accounting to handle their complex financial transactions. 

From multi-channel sales and fluctuating inventory to international taxes and payment processor fees, your online business faces unique challenges. With specialized ecommerce accountants, you can streamline bookkeeping, ensure tax compliance, optimize cash flow, and integrate the best accounting software for ecommerce with platforms like Shopify, Amazon, and WooCommerce.

Without specialized accounting, you might become overwhelmed, which will lead to inaccuracies, compliance issues, and potential losses.

What Do Ecommerce Accountants Handle Each Month?

When doing your books, an ecommerce accountant does more than just record deposits. 

Each month, they also handle:

• Reconciliation per sales channel: They ensure every Amazon disbursement and every Shopify payout are matched to the correct revenue, fees, and refunds. 
• Expense categorization: They ensure accurate expense segregation to avoid lumping expenses (such as ad spend and merchant processing fees) into one category, rendering your P&L unusable for decision-making. They help you see where you’re leaking profits or where it makes sense to spend more aggressively.
• COGS tracking: They record the exact cost of every unit sold (including product cost, inbound shipping, and any prep fees). Remember: If your cost of goods sold is wrong, your margins are also wrong. You then make decisions based on bad data.
• Inventory reconciliation: If you’re using 3PLs, inventory errors directly lead to financial discrepancies. An ecommerce accountant prevents those. For example, if you’re an FBA seller, they help you track stocks lost or damaged by Amazon. Otherwise, any reimbursements you’re entitled to go unclaimed.
• Cash flow monitoring: They flag trends that affect your cash flow, such as months with large inventory buys or slow disbursements, to avoid a cash crunch down the line.
• Monthly reporting: They give you a financial report by the 15th of every month. That gives you time to act on your numbers.

Key Benefits of Hiring an Ecommerce Accountant

Let’s be honest: as much as running an ecommerce business is exciting, it comes with financial headaches. An ecommerce accountant is your best option to keep your business running smoothly. Here’s why hiring one is beneficial:

• Accurate Financial Tracking: Managing multiple sales channels, inventory, and fees can get real quickly. An accountant helps you keep everything organized and accurate.

• Tax Compliance & Optimization: All the taxes, like sales tax, VAT, and income tax, can be a lot to handle on your own. Accountants have expertise in the field and can make sure that you’re compliant while helping you save on deductions.

• Inventory & COGS Management: Knowing the accurate cost of goods sold (COGS) helps you price correctly and boost your profits. 

• Seamless Software Integration: Accountants can seamlessly integrate accounting tools with Shopify, Amazon, or WooCommerce so that everything runs without issues.

• Cash Flow and Profitability Insights: See where your money is going and how to manage it to boost your profitability. With accurate books maintained by an accountant, you can do that.

• Time Saving: With an expert handling your numbers, you can focus on scaling your business without worrying about your books.
  

How to Track Profit Across Sales Channels

Every merchant platform has a different structure. So if you are a multi-channel seller, looking at combined revenue can be misleading.

Here’s how to monitor revenue per sales channel instead:

• Create income accounts by channel: On your bookkeeping software, separate income accounts for Amazon, Shopify, and other channels you’re using. Don’t record all revenue in the same bucket.
• Track channel-specific fees separately: Your FBA fulfillment fees are not the same as Shopify transaction fees. Treat them differently.
• Build a channel-level P&L: This will help you know which channels are worth scaling. Follow this simple formula to determine how each channel is performing:
  • Contribution margin per channel = Revenue – COGS – Channel Fees
• Sync data automatically: Use integration tools like A2X to pull platform payouts directly into your accounting software as categorized entries, rather than lumped deposits.

How to Set Up SKU-Level Profit Checks

Strong top-line revenue also often covers underperforming or unprofitable SKUs. 

Here’s how to check profits per SKU to determine what to keep in inventory:

• Document landed cost per SKU: Record cost before any sale happens. That includes the unit cost, plus inbound shipping, plus packaging.
• Pull FBA fees per SKU: Fees vary by size and weight. Check the FBA fee preview report in Seller Central to see the actual fee per unit, rather than a blended estimate.
• Apply the correct referral fee: Amazon collects a fee for every item sold on its platform. These referral fees range from 6 to 45%, depending on product category. Use the actual rate instead of an average.
• Calculate profit per unit: Get your true profit per unit by deducting landed cost, fulfillment fee, referral fee, and ad spend from the selling price.
• Set a margin floor: General retail averages at 5.61% net margins. But you should set a benchmark based on your category and cost structure. Reprice or renegotiate with your supplier any SKU that falls below that threshold. 

11 Best Accountants for Ecommerce

In a sea of options, what Ecommerce accounting services are good? Multiple firms offer multiple features like financial management, bookkeeping, tax solutions, payroll management, it depends on you what your business needs.

Here are ten of our top ecommerce accounting services picks for you to consider:

1. EcomBalance

EcomBalance is a financial services company that helps you manage your books efficiently. With expertise in platforms like Amazon, Shopify, and eBay, they provide tailored financial management that simplifies your bookkeeping and ensures accuracy. 

They offer:

• Expert bookkeeping, ensuring accurate and up-to-date financial records.
• Smooth integration with third-party platforms like Amazon, Shopify, and more.
• Clear, comprehensive reports such as income statements, balance sheets, and cash flow statements.
• Catch-up and clean-up services to get your financial records organized and compliant.

With their focus on financial clarity and actionable insights, EcomBalance is an excellent choice for businesses seeking reliable bookkeeping support. Their pricing starts from $399/month. 

Sign up today and experience a simplified way of bookkeeping!

2. inDinero

InDinero is a financial team made up of remote and in-house workers. They have CPAs, CFOs, Controllers, bookkeepers, and more that provide a full suite of financial services. The mission of inDinero is to help businesses flourish by making financial management simple and providing actionable insights. 

They offer:

• CFO Services – expert advice, financial planning, budgeting, forecasting, and cash flow management
• Accounting & Bookkeeping Services – Numbers, insights, and analysis 
• Tax Planning & Filing – Minimize liabilities and stress with their comprehensive tax services 

Check out the inDinero pricing page to see their full offers and custom plans. 

3. 1-800Accountant

1-800Accoutant is the largest virtual American accounting firm servicing small businesses.   Their goal is to equip small businesses in all industries with the financial expertise they have gained from working with larger companies. 1-800Accoutant solutions pair CPA expertise with powerful tech. 

Their suite Ecommerce accounting services help you: 

• Maximize tax savings and refunds with more than $12,000 saved on taxes in a year. 
• Run payroll and benefits easily
• Save valuable resources and concentrate on your business through professional bookkeeping 
• Know more about your financials with a dedicated CPA

Check out their free and paid plans on the 1-800Accountant pricing page. 

4. Paro

Paro is a platform created to help businesses and professionals achieve long-term career goals. Their model pairs proprietary AI tech and industry expertise to provide new growth opportunities. Paro business solutions allow for faster problem-solving and better planning for the future. 

Their services include:

• Access to the top 2% of Business Financial Professionals
• Match with an expert faster than other services with proprietary AI talent matching 
• Ecommerce Accounting Services  (with Bookkeeping )
• Business Systems and Process Solutions
• Strategic Advisory
• Financial Planning and Analysis
• Audit and Assurance 
• Tax Services
• Vertical Solutions 

Get started with Paro.

5. Bench Accounting

Bench is one of the most popular accounting services for Ecommerce business owners. They make mastering your financials easy with tools and affordable. Their goal is to be a platform that provides financial insight and peace of mind simultaneously. They want to improve people’s quality of life by allowing them to focus on what they care about in their business. 

Bench solutions include: 

• Financial software – Optimized and easy financial management 
• Dedicated bookkeeping with a team of financial experts 
• Financial reporting – Stay on top of things with monthly financial statements, overviews, and actionable insights 
• Real-time financial data and insights 
• Tax prep and filing – Their Premium plan gives you access to expert tax prep, filing, and year-round tax advisory support.

Visit the Bench pricing page for more info. 

6. Pilot

Pilot is the largest accounting firm for startups in America and is trusted by thousands of companies. Their end-to-end Ecommerce accounting services scale with your needs whether you’re just getting started or have grown to an established company. Their focus is providing the best-tailored customer experience possible with expert teams and a seamless, integrated platform. 

Pilots services involve:

• Bookkeeping – Orderly books and accurate number-crunching with triple-checked financial statements.
• Tax Preparation – Get professional tax help with your income tax filings, 1099s, and more. 
• CFO Services – Get the guidance you need for budgets, metric tracking, funding, and more. 
• R&D Tax Credit – A unique service for R&D heavy companies. They handle tax claims for you. 

Learn more on the Pilot pricing page. 

7. Merritt Bookkeeping

Merritt Bookkeeping is a professional bookkeeping service for people who need the bare essentials. They typically serve US-based small businesses but their clientele includes all sorts of industry types, business and team sizes, and incomes. They tailor accounts to your business using the categories you specify. 

What you get:

• Automated monthly bank reconciliation 
• Bookkeeping in Quickbooks – Includes Quickbooks setup if needed
• Financial reporting through email – You can review this through their custom interface. 
• Same-day replies for any reporting inquiries
• Can directly communicate with your CPA and provide all the info they need
• Discounted catch-up work
• 90-day money-back guarantee

Merritt’s pricing is a flat rate of $190/month. 

8. Bookkeeper.com

Bookkeeper.com has been in the industry for over 30 years. They are a godly company whose mission is to improve the lives of small business owners and workers alike. Their cost-effective, flexible solutions align with their goal of making bookkeeping and accounting attainable for all. Their team of accountants and bookkeepers will partner with you and get to know your business comprehensively. They care about you and your business and are available to answer any questions you may have.

The Ecommerce accounting services include 

• Online Bookkeeping
• Financial Statement Preparation
• Streamlined Bill Pay
• Full-Service Payroll
• Financial Planning and Investments – As well as a full range of other planning services
• Audit Assistance
• Budget Preparation
• Tax Preparation and Advising – Including tax return management
• Business Advising

Take a look at the Bookkeeper.com pricing page to get a full view of their offerings. 

9. BKE (formerly Bookkeeper360)

BookKeeping Express is a professional outsourced bookkeeping service. They were created to help small businesses with affordable financial help. They want to make those back-office procedures easier for clients. Now they have expanded to offering full Ecommerce accounting services for mid-sized businesses. 

What you get with BKE:

• A dedicated BKE team with deep industry knowledge
• A suite of tools and software for optimized financial management
• Accounting System Set Up
• Bank Account Reconciliation
• Bookkeeping and Accounting 
• Monthly Financial Reporting – Access a dashboard and analytics for real-time insights 
• Catch Up and Clean Up Bookkeeping-Reconcile accounts, Bring everything up to date, and Correct Discrepancies
• Bill Pay/Entry – Accounts payable management
• Tax Filing Services – Tax prep, filing, tax returns, full compliance 

To see their value-oriented plans, check out the BKE pricing page. 

10. Xendoo

Xendoo was created by a small business owner to provide owners with financial peace of mind. Their team of tax experts and bookkeepers provides comprehensive and specialized services for your financial success. Xendoo’s technology makes their team 10x more efficient in serving small-mid-sized businesses. 

The solutions that Xendoo offers include:

• Bookkeeping – A dedicated bookkeeper that reconciles monthly 
• Tax – You can be assured that you are always tax-ready and compliant. For an additional fee, they even offer Tax Guidance plus Annual Federal and State Tax Return 
• Catch Up – If you’ve fallen behind on your books they can get you accurate and up to date 
• Fractional CFO Services – This is an add-on service if you need expert guidance and strategy for making informed decisions. 

Learn more about these services on the Xendoo pricing page. 

11. Justworks

Justworks is a unique entry on this list as they offer more than just Ecommerce accounting services. On top of payroll services and compliance support, they also offer employee benefits and HR services. Justworks is about handling busy work so that you can pursue your passion. They also want to make sure your team is happy so you can work better together towards greater goals. 

What do you get with Justworks?

• Payroll Services – Online payroll includes benefits deductions, tax withholdings, payments to vendors and contractors, and the option for time-tracking integration. 
• Employee Benefits – Take care of your team and access more affordable benefits deals. These include 401ks and insurance (medical, dental, vision). 
• HR Tools – Access integrated HR software to better manage your team. 
• Compliance Support – They can help report and remit your federal, state, and local payroll taxes, and file W-2s and 1099s. 
• 24/7 support is always at the ready to help 

Check out their plans on the Justworks pricing page. 

Sales Tax Rules That Can Hurt Ecommerce Brands

Sales tax is where ecommerce sellers usually get caught off guard. One common reason is that the rules changed in 2018, and many business owners still haven’t fully caught up.

Before the 2018 South Dakota v. Wayfair ruling, you only owed sales tax in states where you physically sold goods.

Now, sellers are required to collect and remit sales tax based purely on sales volume, regardless of physical presence.

So what creates nexus (or a taxable connection between your ecommerce business and the state) for ecommerce sellers?

• Crossing a state’s revenue threshold: Most states set a threshold of $100,000 in sales, but the numbers vary. Always check each state you’re selling in individually.
• FBA inventory storage: If Amazon stores your stocks in a fulfillment center in any given state, you likely have nexus in that state, regardless of where you’re based.
• Having your own warehouse or employees: If you store inventory in your own warehouse or have employees managing stocks, you automatically have nexus in that state.

But here’s where sellers get tripped up:

• Marketplace facilitators don’t cover website sales: Platforms like Amazon, Shopify, and eBay collect and remit sales tax on your behalf in most states. In sales tax laws, they’re called “marketplace facilitators”. However, if you sell directly through your own website, you are responsible for tax compliance on those sales.
• Product taxability varies: Some products are tax-exempt in some states but taxable in others. For example, clothing is exempt in Pennsylvania but taxable in most other states. Digital goods also have their own tax rules. There’s no consistent pattern.
• Tax liability accumulates: States can audit unpaid taxes going back three to four years. If you’ve crossed a threshold and haven’t registered, your unpaid taxes build up.

What to do to avoid sales tax problems:

• Automate tax processes: Use tools like TaxJar to identify states you have nexus in and collect sales tax on platforms where you sell.
• Register where you have nexus: Register in every state where you cross an economic threshold or sell goods.
• Work with a CPA specializing in ecommerce: A generalist CPA often misses FBA nexus and marketplace facilitator rules. Work with a CPA who specializes in ecommerce tax services.

How to Choose the Best Ecommerce Accounting Services

If you think that an accountant is crunching your numbers and recording your books, then you might not find the best fit for your business. An ecommerce accountant should know about the unique challenges online businesses face. Here’s what you should look for:

• Ecommerce Expertise: This should be the core factor when you’re hiring an accountant. Not all accountants are familiar with online business models, so finding an expert who knows platforms like Shopify, Amazon, eBay, and WooCommerce is your best bet.
• Sales Tax Knowledge: With ever-changing tax laws across different states and countries, your accountant should be well-versed in sales tax compliance.
• Inventory & COGS Management: A good ecommerce accountant will help you track inventory costs accurately and improve profit margins.
• Scalability: Your accountant should offer insights as your business grows and help with forecasting, budgeting, and financial strategy.
• Transparent Pricing: To avoid any surprises, choose a service that offers clear pricing and no hidden fees.
• Great Communication: You need someone who can explain financial matters in a way that makes sense to you, not just through a bunch of numbers at you.

Frequently Asked Questions (FAQs)

Here are some commonly asked questions that might be helpful to you.

What Are the Different Methods of Accounting for Ecommerce?

The methods of accounting are based on when revenue is recorded. The two methods are cash and accrual. If it is recorded the moment you receive or pay money, it’s a cash basis. If you record it the moment you receive a bill or issue an invoice to a client, it’s accrual. You can also think of accrual as a credit basis system. Learn more about the differences between cash vs accrual methods of accounting.

Should I Hire a Professional Accountant?

Professional accountants are valuable if you want to free up your resources, save money in the long run, get more organized financials, and let someone else manage the tax stress. 

What Software Can I Use for Ecommerce Accounting?

Quickbooks and Xero are two that we recommend. Learn more about these options and more  in our article on the “6 Best Accounting Software Picks for Ecommerce Companies”

Can I Do My Own Accounting for My Ecommerce Business?

Sure, you can! DIY accounting is even recommended for businesses that are just starting out and don’t have a lot of transactions to record. However, when your business grows, we do recommend hiring a bookkeeper and considering one of the accounting services on this list. 

How Do I Know If I Need an Accountant for My Ecommerce Business?

If you’re wondering whether hiring an accountant is worth it, analyze these situations:

• Your finances are becoming too complex: Managing multi-channel sales, handling inventory, and dealing with expenses can quickly become overwhelming. 

• Sales tax compliance is challenging: Selling in multiple states or countries and keeping up with tax laws is a full-time job on its own.

• No time for bookkeeping: If tracking expenses, reconciling accounts, and managing cash flow is eating up time you could be spending on growth, it’s time you get help.

• Missing tax deductions: An accountant can spot opportunities to save money on taxes that you might not even know exist.

• Business is expanding quickly: More sales mean more financial complexity. An accountant can handle such situations and help you scale smoothly.

What Mistakes Should I Avoid When Working with an Ecommerce CPA?

Once you’ve found the right accountant, you should avoid these common mistakes to make the most out of their expertise:

• Not keeping proper records: Even the best CPA can’t help if your receipts, invoices, and financial data are a mess. So you need to keep things organized!

• Ignoring their advice: If they recommend changes to improve your financial health, take them seriously, as they have some expertise in the field.

• Only consulting during tax season: A good CPA does more than just taxes—they help year-round with budgeting, cash flow, and growth strategies.

• Not discussing e-commerce-specific needs: Make sure they understand the unique challenges of online businesses, like marketplace fees and inventory tracking.
• Skipping regular check-ins: Don’t just talk to your accountant once a year. Regular check-ins can help you avoid financial surprises.

Conclusion

There you have it! Believe it or not, you can take control of your finances by handing them over to someone else. A professional accounting service has the tools, resources, personnel, skills, and experience to take your financial management to the next level. Why not go and check them out for yourself?