Ecommerce accounting for Amazon, Shopify, Walmart & eBay sellers
Ecommerce Accounting Services for $2M–$50M US Businesses
You sell on several platforms and revenue is growing, but your books are a mess. Payouts don’t match, your cost of goods sold (COGS) is wrong, and sales tax keeps you up at night because your bookkeeper doesn’t know ecommerce.
Ledger Labs is the outsourced ecommerce accounting team for online brands making $2M–$50M on Shopify, Amazon, Walmart, and beyond. We match every payout to its deposit, keep inventory on the balance sheet until a unit sells, and track the states where you have crossed a sales-tax threshold. We also serve inventory-led ecommerce, consumer packaged goods (CPG), manufacturing and distribution businesses across the United States.
2,246+
Clients served
12 +
Years in industry
150 +
Strong team
WHAT WE FIX
What Our Ecommerce Accounting Services Fix
Many ecommerce brands only learn their records are wrong at tax time or when they seek funding. Unmatched payouts, wrong cost of goods sold (COGS) and surprise sales tax bills can quietly cost thousands. Here’s how we fix them.
Problem: Bank deposits don't match sales reports, and processor fees eat your margin.
Fix: We reconcile each settlement, splitting payouts into gross sales, fees, refunds and tax.
Problem: Your profit and loss (P&L) shows fake profit because inventory is expensed when bought, not when sold.
Fix: We carry inventory as an asset and move it to COGS only when a unit sells.
Problem: Nexus, marketplace facilitator rules and filing deadlines keep you up at night.
Fix: We watch nexus (when a state can require you to collect sales tax) in all 50 states, register you and file on time.
Problem: You don't know which products actually make money after fees and ad spend.
Fix: Per-SKU contribution margins after shipping, platform fees, fulfillment, and ads.
Problem: You can't see cash position, channel profit, or ad ROI in real time.
Fix: Dashboards, and books close one week after month end, with channel-level breakouts.
Problem: Your balance sheet is worthless to a lender, and you're one audit from a big liability.
Fix: Documented financials, with a schedule or work paper behind every material balance-sheet line.
Problem: Refunds and chargebacks are double-counted or land in the wrong month.
Fix: Refunds tied to original orders; chargebacks tracked separately, by channel.
Problem: You lose hours every month to bookkeeping and fixing integration issues.
Fix: We take the whole ecommerce accounting function off your plate.
WHAT WE HANDLE
Ecommerce Bookkeeping Services We Handle For You
Stop spending hours every month on bookkeeping. Our outsourced ecommerce accounting services handle the full financial picture, reconciled to the platform, not just the bank, so you can focus on growth.
- Inventory & COGS Tracking
Inventory carried as an asset and released to COGS only when a unit sells, so margins reflect what moved, not what you bought. Shrinkage and write-offs tracked separately. For clothing and apparel sellers, see our accounting services for clothing brands.
- Sales Channel Reconciliation
We reconcile platform settlement reports, not just bank deposits, splitting Amazon payouts into gross sales, referral fees, Fulfillment by Amazon (FBA) fees, refunds, and tax, and clearing stranded balances monthly. For Shopify stores, our Shopify accounting services tie every order to your bank feed the same way, matching each payout to the transaction export Shopify provides for every payout.
- Revenue Recognition Across Platforms
Revenue recorded when the order ships, not when cash lands, with pre-orders, subscriptions, and gift cards deferred until earned.
- Payment Gateway Fee Accounting
Stripe, PayPal, Shopify Payments, and marketplace fees, such as Amazon's referral and FBA fees, booked as expenses, not netted from revenue, so you see true sales and true processing cost.
- Refunds, Returns & Chargebacks
Refunds tied to original orders and dates; chargebacks tracked separately with representment outcomes, so returns don't distort the wrong month.
- Multi-State Sales Tax Tracking & Filing
Nexus monitored across all 50 states, platforms configured to collect correctly, and returns filed on schedule. Thresholds vary by state: most use $100,000, Alabama and Mississippi use $250,000, and California, New York and Texas use $500,000 (New York also requires more than 100 sales), as the Streamlined Sales Tax Governing Board's remote seller chart shows. The full registration-to-filing cycle across every channel you sell on is set out on our sales tax services for US businesses page.
- SKU-Level Profitability Analysis
Contribution margin per product after shipping, platform fees, fulfillment, and ad costs, so you know what to grow, reprice, or cut.
- Accounts Payable & Vendor Payments
Supplier bills, third-party logistics (3PL) invoices, and inventory purchase orders (POs) entered and approved against your cash position, so you don't commit to deposits you can't afford.
- Payroll & Contractor Tracking
Payroll assigned to the right departments and 1099 contractors tracked all year, so January is filing, not sorting.
- Monthly Financials & Cash Flow Reporting
P&L, balance sheet, and cash flow delivered when the books close, one week after month end, with channel-level breakouts and a written note on what changed and why.
- Tax Compliance & Filing Support
The same team keeps your books and files your return, no handoff, no year-end cleanup, no second firm re-learning your business.
Our exclusive 16-chaptered, long-awaited ebook “Accounting for Internet Sellers: An Insanely Detailed Guide” is now available
Authored by Gary Jain. Put together by experts at Ledger Labs®
HOW IT WORKS
What Working With Our Ecommerce Accountants Looks Like
Ecommerce Accounting Assessment
We start by diving into your entire multi-channel setup: Shopify, Amazon, eBay, Stripe, PayPal, and everything in between. As ecommerce specialist accountants, we analyze how revenue moves, how inventory is tracked, and where the numbers stop lining up. We surface what's broken and build a plan to clean it up- no guessing, just a clear roadmap to accurate, scalable financials.
Action Plan Implementation
Once the plan is set, we execute, syncing your storefronts with your accounting software, reconciling sales deposits, and mapping refunds, discounts, and inventory movements correctly. We also build systems to track multi-state sales tax obligations, plus documentation to support your numbers in an audit, diligence, or platform review.
Automation Built for Ecommerce Ops
Where automation makes sense, we use it, syncing sales channels to your accounting platform, building auto-reconciliation workflows, and streamlining tax reporting. We've built automation for fast-scaling Shopify brands, Amazon sellers, and omnichannel operators, so clean data flows without the manual work.
Live Reporting That Tracks What Matters
You'll spend less time chasing numbers. We build real-time dashboards tracking cash, margins, ad spend, and SKU-level performance across every channel, so you get clarity without logging into five dashboards.
Reviews
Here's What Happens When You Work With Us!
5.0
From 20 reviews
Patrick Hensley
Head of Product at AtlasPeak Technologies
reviewed on 27/3/2026
Fractional CFO Service that made financial planning easier
Hiring a full-time CFO wasn’t practical for us, but we still needed high-level financial guidance. Ledger Labs’ fractional CFO service gave us exactly that. They helped us set budgets, improve cash flow management, and prepare for investor discussions.
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Kevin Hollis
Senior executive at Canyon Peak Outfitters
reviewed on 17/7/2026
Great Experience with Ecommerce Accounting
We’ve partnered with Ledger Labs for about 18 months to manage bookkeeping and ecommerce accounting. Selling across Shopify and Amazon made reconciliation challenging, and our reports were never completely accurate. Their team streamlined the entire process and helped us understand where our profits were actually coming from. They’re easy to reach, communicate clearly, and resolve issues quickly.
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Ian Delaney
Project Assistant at Fairmont Systems Inc
reviewed on 20/6/2026
Great Bookkeeping Support
We’ve been working with their bookkeeping team for a little over 2 years. Before that, our books were constantly behind, and I never felt confident looking at our financial reports. The team helped clean up historical transactions and built a process that keeps everything updated each month.
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Reviews (38)
5.0
Trevor James
May 08
We contacted Ledger Labs when our QuickBooks records became difficult to manage internally. There were duplicate entries, unreconciled transactions, and several months of pending bookkeeping work. Their team handled the cleanup process professionally and explained every correction clearly. After the cleanup, they also helped us establish a monthly bookkeeping workflow that made reporting much more organized.
Jason Carter
Apr 25
Ledger Labs has been a reliable accounting partner for our business. Their team is responsive, organized, and always delivers work on time. Highly recommended for startups and growing companies.
Gregory Walsh
Apr 04
We run a mid-sized Shopify store, and our books were always a mess, especially with payouts and fees. Ledger Labs cleaned everything up, and now our monthly reports actually make sense. It’s much easier to see where we’re making money and where we’re not.
Team You Can Count On
Gary Jain
Founder & CEO
Gary is the Founder & CEO of Ledger Labs, which he started in 2014. With over a decade in accounting, he oversees CFO services, ERP accounting, and finance automation for ecommerce, CPG, and manufacturing businesses in the United States. He is also a council member of Forbes.
Allison Rinehimer
CPA | Operations Manager
Allison is a (CPA) and a member of the AICPA. She oversees operations at Ledger Labs, where every close follows a written checklist with a named owner and deadline. With experience in both public and private accounting, she builds scalable systems that support fast-growing ecommerce businesses.
Matt Hidalgo
Accountant
Matt has worked in accounting across ecommerce, SaaS, and technology. He specializes in financial reporting, month-end close management, and ERP transitions, including NetSuite. Matt supports clients' monthly close and reporting, so they have financials to use in growth decisions.
Why Sellers Switch to Our Ecommerce Accounting Team
Over 2,000 ecommerce businesses trust us with their books. Here’s the real difference:
| Feature | Generic Bookkeeper | DIY Accounting | Ledger Labs |
|---|---|---|---|
| Platform-Synced Bookkeeping | Manual imports with frequent errors and platform mismatches | You spend hours every month downloading CSVs and reconciling | Automation-supported reconciliation across Shopify, Amazon, Stripe, and PayPal, mapped to your chart of accounts |
| Accurate COGS & Inventory Tracking | Generic cost assumptions with no inventory reconciliation or per-product visibility | You’re guessing inventory values in spreadsheets | SKU-level COGS tracking with real-time inventory valuation and true landed cost calculation |
| Multi-Channel Financial Consolidation | Disorganized reporting split between systems and spreadsheets | Separate spreadsheets per channel, you’re drowning in data | Clean consolidation across sales channels with unified reporting and seamless data flow |
| Sales Tax Compliance & Filing | Missed thresholds and late filings due to manual oversight or outdated systems | You’ll deal with it when audited (hopefully never) | Nexus monitoring, sales tax mapping, and returns prepared against a tracked filing calendar across your platforms |
| Profitability Reporting & SKU Analysis | Flat P&Ls with no breakdowns or actionable visibility | You know revenue, but not profit by product or channel | Clear dashboards showing profit margins by SKU, channel, ad campaign, and fulfillment method |
| Return & Refund Tracking | Refunds overlooked or double-counted, distorting revenue | Manually tracking refunds in separate spreadsheets | Fully reconciled returns, chargebacks, and partial refunds are reflected accurately in your financials |
| Real-Time Cash Flow Monitoring | Delayed cash flow statements and a lack of forecast accuracy | You’re guessing if you can afford that $200K inventory order | Dashboards on cash flow, payouts, liabilities, and working capital across all processors |
| Documented Financials & Support | Vague notes, missing context, and last-minute | "I'll figure it out at tax time." (famous last words) | Well-organized, documented entries with supporting detail for every transaction |
| Ecommerce Specialist Access | Slow turnaround from generalized support teams with limited ecommerce experience | Google searches and Reddit forums are your "advisors." | Slack/email access to your dedicated ecommerce accountant for fast answers and strategic insight |
| Monthly Close Timeline | Often arrives too late to act on the data | Never (or quarterly at best when you remember) | Books close one week after month end. |
| Monthly Cost | Varies by provider, and the scope is often basic bookkeeping only | $0 cash, but many hours of your time every month | Fixed monthly plans for comprehensive ecommerce accounting — see our pricing page |
| Setup & Onboarding Time | A slow start, if they understand ecommerce at all | Ongoing chaos with no clear system | Onboarding from as little as two weeks to a maximum of twelve, depending on the state of your books and systems. |
Accounting Software We Work In
Our Testimonials
Hear from More Business Owners Who Were in Your Exact Position
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FAQ
Ecommerce Accounting Questions We Get A Lot
1. What ecommerce platforms do you work with?
Ledger Labs works with all major ecommerce platforms: Amazon (FBA & FBM), Shopify, Walmart, Etsy, eBay, WooCommerce, TikTok Shop, BigCommerce, Target Plus, Facebook Marketplace, and any channel you sell on. We also integrate with payment processors like Stripe, PayPal, Square, and Shopify Payments. Newer marketplaces are covered as well; our accounting services for Temu sellers set out how Temu fees and transactions are handled. For the systems behind your store, see our guides to inventory management for ecommerce, Xero for Amazon FBA sellers, and NetSuite for ecommerce, plus our NetSuite ecommerce reporting white paper. For Etsy stores, we reconcile Etsy Payments deposits against orders and separate transaction, processing, listing, and Offsite Ads fees; for WooCommerce stores, we match orders to each payment gateway (such as WooPayments, Stripe, or PayPal), since payouts arrive separately from each one.
2. What does your monthly bookkeeping service for ecommerce sellers include?
Ledger Labs’ ecommerce bookkeeping runs on a fixed monthly schedule, so you get the same reports on the same date every month:
- Sales Reconciliation: we match sales from Shopify, Amazon, Walmart, eBay, Stripe, and PayPal to your bank deposits, splitting each payout into gross sales, fees, refunds, and collected sales tax.
- Inventory & COGS: we update inventory and COGS (including shipping, duties, and tariffs), carrying inventory as an asset and recognizing COGS only when sold, using Weighted Average or FIFO.
- Financial Reporting: we deliver your P&L, balance sheet, cash flow statement, and SKU-level margin report one week after month end, with a summary of what changed.
3. How do you handle sales tax compliance across multiple states?
Ledger Labs monitors your nexus footprint across all 50 states, registers you where needed, configures your platforms to collect correctly, and files returns on time, proactively tracking threshold changes so you stay compliant and avoid penalties. Amazon collects and remits state sales tax on your marketplace orders as the marketplace facilitator, as Amazon’s marketplace tax collection page explains, but that doesn’t cover your Shopify or wholesale sales, and some local taxes fall outside it. We also split every marketplace payout into gross sales, fees, refunds, and collected sales tax, so what you report matches what you actually collected.
4. Do you track profitability by product or SKU?
Ledger Labs provides SKU-level profitability reports showing margin by product, sales channel, and fulfillment method, after all costs and fees, so you know exactly which products make money and which don’t. We build those margins from landed costs, including shipping, duties, and tariffs, so each SKU’s profit reflects what it really costs to sell.
5. Can you help with inventory management and COGS?
Ledger Labs tracks inventory as an asset, calculates accurate COGS including landed costs (shipping, duties, freight), and provides real-time inventory valuation. We also integrate with inventory systems like Finale, Inflow, and SkuVault. Inventory stays on the balance sheet, and COGS is recognized only when items sell, using Weighted Average or FIFO.
6. What accounting software do you require us to use?
Ledger Labs works with QuickBooks Online, Xero, NetSuite, Odoo, and Sage Intacct. If you’re already on one, we’ll optimize it; if you’re starting fresh, we’ll recommend the best fit for your size and complexity. Shopify stores already on Xero can see the payout, refund, fee and inventory workflow on our Xero bookkeeping for Shopify businesses page.
7. How do you integrate with my existing tools and systems?
Ledger Labs works with your sales channels, payment processors, inventory systems, and ad platforms using tools like A2X, Link My Books, and native APIs, with human review of exceptions. It’s the same approach behind our automated bookkeeping services.
8. How will I communicate with my accounting team?
Every Ledger Labs ecommerce client gets direct access to a dedicated ecommerce accountant via Slack or email for quick questions, plus monthly review calls to walk through your financials and strategy. Response time is typically within 24 hours. Each review call covers your P&L, balance sheet, cash flow statement, and SKU-level margin report, with a summary of what changed.
9. How long does onboarding take?
Ledger Labs onboarding takes from two weeks to a maximum of twelve, depending on the state of your books and systems. We connect your sales channels, clean up historical data if needed, set up a proper chart of accounts, and deliver your first monthly financials.
10. Do you provide year-end tax returns?
Ledger Labs prepares year-end business returns for ecommerce sellers (Form 1120, 1120S, 1065, Schedule C) and maximizes ecommerce-specific deductions. Because we manage your books year-round, tax season is seamless, not chaotic. We also track your sales tax nexus during the year, so income tax and sales tax filings draw on the same reconciled numbers.
11. Should I cost my inventory with weighted average or FIFO?
Weighted average suits a small catalog with stable supplier prices. It keeps cost of goods sold (COGS) simple and accurate enough. FIFO suits many SKUs, frequent reorders, or supplier prices that move between orders, because it keeps each unit’s margin true. When freight, duty and tariffs are a meaningful share of what a unit costs, we add a landed-cost layer. For your books, gross margin then reflects what each unit actually cost, not an average that hides price swings.
12. Do I need a settlement connector like A2X, or is a direct connection enough?
We recommend a direct platform-to-ledger connection if you sell on one channel and each payout is a simple deposit. If you sell on several channels, or your payouts bundle fees, refunds, reserves and tax, a settlement connector such as A2X earns its cost, because it splits each payout before it reaches the ledger. For your books, every bank deposit then ties back to the orders and fees behind it.
News & Blogs
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See What Happens When You Work With Us
From saving thousands to scaling fast, these stories highlight how we help businesses grow smarter with real financial strategy and execution.
Empowering Business Confidence Through Precision and Insight
Navigating Financial Complexity to Secure Investment
Between Shopify, Amazon, and three payment processors, our deposits never matched our sales. I genuinely didn't know what we'd actually made. Ledger Labs reconciled everything down to the settlement level, splitting out fees, refunds, and tax. For the first time, my books match my stores to the cent.
Colton Reyes Founder