Top Ecommerce Bookkeeper Firms for Sellers (Amazon, Shopify, Walmart & Beyond)

If you sell on Amazon, Shopify, Walmart or a mix of marketplaces, this is the ultimate guide for ecommerce bookkeepers and sellers seeking bookkeeping solutions. Your ecommerce bookkeeper has to handle things a “normal” generalist bookkeeper rarely sees: messy channel payouts, marketplace fees and chargebacks, COGS tied to inventory movements (not just purchases), cross-border sales tax, and a stack of apps gluing it all together. The right ecommerce bookkeeping partner keeps those moving parts clean so your P&L, balance sheet, inventory and cash actually make sense. This helps you to make smarter decisions with confidence.

Below is a practical guide to leading ecommerce bookkeeping firms. Learn what they’re best at, who they serve, and how they’re different, followed by a checklist to choose the right bookkeeper for your ecommerce business.

What to Look for in an Ecommerce Bookkeeper

Marketplace fluency

Amazon (AWD, FBA, and FBM), Shopify, Walmart, Etsy, TikTok Shop, and eBay each pay out and report differently. You want a firm that regularly reconciles marketplace statements to your books, not one that treats payouts as “sales.” Choosing an ecommerce platform that integrates well with your bookkeeping software is essential for streamlined financial management and accurate record-keeping.

Inventory & COGS on accrual

Accurate landed costs, purchase timing, freight/duties, and returns must roll into COGS. Cash-basis COGS can wildly distort margins. Payment processing fees should also be categorized appropriately, as they are often considered part of COGS or as a deductible business expense.

Sales tax & nexus awareness

You may need registrations and filings across multiple states/countries even with marketplace facilitator laws in play. Proper account management, including tracking sales tax payable, is crucial for compliance.

App stack know-how

Make sure your bookkeeper's app stack allows for keeping track of all financial transactions, including sales, expenses, profits, and specific categories like advertising costs and payment processing fees, to ensure nothing is missed. Seamless integrations between apps is critical to getting clear and accurate numbers. ConnectBooks for P&L reports, accounting and channel summaries; QuickBooks Online or Xero for expense capture, payroll & bill pay; and inventory systems like ConnectStock to track inventory age and value.

Clear deliverables & cadence

Your bookkeeper should close by a set day each month, with standardized reports (P&L by channel/SKU, cash flow, aged payables/receivables), and a recurring review call. Tracking sales is a key function for accurate financial reporting and business growth.

Scalability

Ensure your bookkeeper has the ability to add AP/AR, inventory support, and fractional CFO services as you grow.

The Benefits of Ecommerce Bookkeeping

Ecommerce bookkeeping is an integral part of running a successful ecommerce business. By maintaining accurate and up-to-date financial records, ecommerce businesses gain a clear picture of their sales revenue, expenses, aging inventory, and overall financial health. This level of financial reporting allows business owners to track performance, spot trends, and identify areas where they can optimize operations or reduce costs.

Effective ecommerce bookkeeping also plays a crucial role in managing cash flow, ensuring that businesses have the funds needed to cover expenses, invest in new opportunities, and weather seasonal fluctuations. With reliable financial records, ecommerce entrepreneurs can make informed financial decisions, from setting budgets to planning for growth.

Another key benefit is tax compliance. Accurate bookkeeping helps ecommerce businesses stay on top of their tax obligations, making it easier to file returns and avoid fines or penalties. By keeping detailed records of sales, expenses, and write offs, businesses can ensure they are prepared for tax season and can take advantage of any available deductions.

Ultimately, ecommerce bookkeeping empowers businesses to make smart decisions, improve profitability, and maintain a competitive edge in the fast-paced world of online sales. Whether you’re just starting out or managing a rapidly growing online store, investing in solid bookkeeping practices is essential for long-term success.

Common Mistakes in Ecommerce Bookkeeping

Ecommerce bookkeeping can be time consuming and complex, especially for businesses new to online sales or those experiencing rapid growth. One of the most common mistakes ecommerce businesses make is failing to properly track inventory purchases, which can lead to inaccurate cost of goods sold and distorted profit margins. Neglecting to regularly reconcile bank statements is another pitfall that can cause discrepancies between your financial accounts and actual cash on hand.

Another frequent error is misclassifying or misunderstanding sales tax, which can result in non-compliance with tax laws and unexpected fines. Many ecommerce businesses also struggle to keep up with changing tax obligations, such as economic nexus rules, which can vary by state and sales channel. These challenges can lead to inaccurate financial reports, making it difficult to assess the true financial health of the business and potentially resulting in poor or uninformed decisions.

To avoid these common mistakes, ecommerce businesses should leverage reliable accounting software to automate and streamline bookkeeping tasks. Hiring a certified bookkeeper or outsourcing to a dedicated team of ecommerce bookkeepers can also help ensure that financial records are accurate and up to date. By staying proactive and investing in the right tools and expertise, businesses can avoid costly errors, stay compliant, and focus on growth.

9 Ecommerce Bookkeepers Sellers Should Know

1) Bookkeeper360

Best for: Sellers that want a broad, US-based team that pairs bookkeeping with CFO, payroll/HR and sales tax registrations & filings.

Why they stand out: Bookkeeper360 maintains a dedicated ecommerce practice. Their expertise goes across multiple ecommerce platforms and explicitly includes income tax filings, sales tax registrations, sales tax filings, and nexus determinations in addition to bookkeeping and advisory.

Good fit if: You want an all-in-one accounting partner (bookkeeping + tax + payroll + advisory) that knows ecommerce tooling and compliance.

2) bookskeep

Best for: Amazon and Shopify brands that want Profit First cash-management baked into the bookkeeping.

Why they stand out: bookskeep is deeply tied to the Profit First methodology and explicitly markets “Mastery Level Profit First Professionals,” along with streamlined ecommerce bookkeeping packages. They also emphasize fluency with Amazon Seller Central data so you can quickly answer questions on returns, inventory and profit structure. Their “SmartBooks” package targets $1M+ sellers; “SmartStart” is a setup track for DIY-inclined owners.

Bookskeep's typical stack & services include: QuickBooks Online, ConnectBooks, monthly closes, management reports, advisory built around Profit First for Ecommerce Sellers, and Amazon and Shopify-specific accounting support.

Good fit if: You want disciplined cash management alongside accurate books, with a knowledgeable and helpful team that clearly understands Amazon and Shopify.

3) LedgerGurus

Best for: Multichannel brands that need an end-to-end ecommerce accounting team with inventory consulting and sales tax support.

Why they stand out: LedgerGurus is an ecommerce specialist firm with defined Amazon accounting packages and inventory consulting. Their services include: Reconciliation of sales channels and payment processors, accrual COGS, inventory management, monthly financials by the 20th, plus optional services for sales tax, inventory consulting, AP/AR, payroll, and catch-up/cleanup. Pricing packages start at $350/month. They do not file income tax returns, focusing instead on day-to-day accounting and decision support.

Good fit if: You want a dedicated ecommerce team that can scale from bookkeeping to sales tax and inventory advisory under one roof.

4) CapForge

Best for: Amazon sellers who want fixed, flat-rate pricing, no long-term contracts, and a money-back guarantee.

Why they stand out: CapForge has a long-standing Amazon seller practice. They offer month-to-month services (no contract), and a 100% money-back guarantee. Plus, their team has process knowledge around matching Amazon reports to tax filings and true-profit clarity.

Good fit if: You want predictable costs, fast onboarding, and a firm comfortable speaking “Amazon” in plain English.

5) Pinit Bookkeeping

Best for: Amazon and multi-channel operators who want bookkeepers experienced in ConnectBooks and comfortable with wholesale/3PL complexity.

Why they stand out: The Pinit Bookkeeping team is described as “experts in ConnectBooks” with experience supporting 3PL, wholesale, Amazon & multi-channel operations (useful if your business moves beyond single-channel DTC).

Good fit if: Your accounting depends on ConnectBooks and you need a bookkeeper used to multi-node operations (3PLs, wholesale, multiple marketplaces).

6) Jones & Cosman

Best for: Shopify and Amazon brands that value transparent packaging and pricing from a boutique ecommerce-only accounting firm.

Why they stand out: Jones & Cosman CPAs markets itself squarely to ecommerce sellers and focuses on establishing trust and buillding relationships with their clients. Their package offerings are dedicated to ecommerce bookkeeping, and their pricing is transparent on their website which helps you budget and compare. The co-founder, Rob Cosman, is not only a CPA and entrepreneur, but he is also an Amazon seller.

Good fit if: You prefer a boutique firm with ecommerce focus, clear scope, and upfront pricing expectations.

7) Seller Accountant

Best for: Amazon and multichannel brands that want ecommerce-only bookkeeping with the option to layer on fractional CFO.

Why they stand out: Seller Accountant focuses on ecommerce bookkeeping, cleanup, and fractional CFO services for online sellers, making them a fit for brands moving from “order taker” to “data-driven operator.”

Good fit if: You’ve outgrown basic bookkeeping and want someone to help you interpret KPIs, cash conversion cycles, and channel profitability.

8) CedarRock Advisory Group

Best for: Sellers who want ConnectBooks-centric bookkeeping and standardized ecommerce processes.

Why they stand out: The CedarRock Advisory Group ecommerce bookkeeping services include receipt processing, financial reporting, and ConnectBooks usage.

Good fit if: You’re already on ConnectBooks (or planning to be) and want a team built around that integration pattern.

9) Bottom Line Management

Best for: Sellers prioritizing a tight integration with ConnectBooks for data accuracy between marketplaces and accounting.

Why they stand out: Bottom Line Management is presented as a ConnectBooks company offering high-quality bookkeeping solutions tailored for the needs of eCommerce businesses. If your workflow already centers on ConnectBooks for channel-to-GL mapping and reporting, this alignment is a differentiator.

Good fit if: You rely on ConnectBooks and want a bookkeeping team optimized around that ecosystem.

How to Choose the Right Partner for Your Bookkeeping Services

For small business owners, especially those new to ecommerce, hiring an ecommerce bookkeeper is critical to have accurate financial data. It takes a lot of time and expertise to manage business finances, track revenues, and avoid the common pitfalls that cause many ecommerce businesses to fail. Regularly reviewing revenues and loss statements helps assess business performance and provides insight into the company's finances, supporting better decision-making and long-term success.

7 Question Checklist

Here are some questions to help you find the right ecommerce bookkeeper for your ecommerce business:

1. Which channels do you sell on, and how will they reconcile them?
   Ask for a walkthrough of how Amazon/Shopify/Walmart payouts are summarized and tied to your General Ledger (GL) each month, including fees, chargebacks, and gift card liabilities.
2. How do they handle inventory and COGS?
   Look for accrual accounting with landed costs and returns impact, plus a plan for when you outgrow spreadsheets and need an inventory system. Many firms will meet you where you are and help implement inventory management software if needed.
3. What’s the close cadence and the deliverables?
   You want a committed close date (e.g., by the 20th) and reports segmented by channel/SKU.
4. Can they support your sales-tax footprint?
   As a professional ecommerce seller, you’ll likely have multi-state nexus. Make sure they can help you collect sales tax in every US state where you have nexus, as compliance with each state's requirements is essential for online sellers.
5. Do you want Profit First or CFO advisory?
   If your focus is cash discipline, bookskeep is built around Profit First. If you need KPI storytelling and forecast/FP&A alongside bookkeeping, Seller Accountant and LedgerGurus offer fractional CFO/advisory options. Accurate bookkeeping is crucial for informed decision making, enabling ecommerce sellers to understand their financial health and make better business choices.
6. What are the terms and price structure?
   LedgerGurus publishes a starting price; Jones & Cosman shows ecommerce pricing packages; CapForge promotes flat-rate, month-to-month with a money-back guarantee. Use those benchmarks when evaluating proposals.
7. What does onboarding look like?
   Ask how they’ll clean up the past, set up integrations, and document your workflows (AP, inventory receipts, returns handling). You want a defined project plan and a realistic first-90-days roadmap. Many of the firms above outline structured onboarding flows on their websites.