Ecommerce accounting for Amazon, Shopify, Walmart & eBay sellers

Ecommerce Accounting Services for US Businesses

You sell on different platforms, and your revenue is growing, but your accounting is 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 understand ecommerce.

Ledger Labs is the outsourced ecommerce accounting team for online brands making $1M–$20M on Shopify, Amazon, Walmart, and beyond. Led by licensed CPAs and an IRS Enrolled Agent, we’re the accountant for ecommerce businesses that generalists can’t match, a firm of certified accountants, not just bookkeepers.

2246 +

Happy Clients

12 +

Years in industry

150 +

Strong team

WHAT WE FIX

What Our Ecommerce Accounting Services Fix

Many ecommerce brands don't realize their financial records are incorrect until tax time or when they seek funding. Issues like unmatched payouts, incorrect cost of goods sold (COGS), and unexpected sales tax obligations can quietly cost you thousands. Here’s how we can help fix these problems.

Problem: Bank deposits don't match sales reports, and processor fees eat your margins.
Fix: We reconcile platform settlements, splitting payouts into gross sales, fees, refunds, and tax.

Problem: Your P&L shows fake profit because inventory is expensed when purchased, not when sold.
Fix: We carry inventory as an asset and release it to COGS only when a unit actually sells.

Problem: Nexus, marketplace facilitator rules, and filing deadlines keep you up at night.
Fix: We monitor nexus across all 50 states, register you, and file on schedule.

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 a monthly close by the 15th, with channel-level breakouts.

Problem: Your balance sheet is worthless to a lender, and you're one audit from a big liability.
Fix: Clean, documented, audit-ready financials that hold up in diligence.

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 20+ hours a 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 20+ hours a 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.

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, 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 stay compliant with multi-state and international tax, plus documentation that stands up under 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 never chase numbers again. 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 16 reviews
Patrick Hensley
Head of Product at AtlasPeak Technologies
reviewed on 27/3/2026
Patrick Hensley
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.
Budget
5.00
Schedule
5.00
Quality
5.00
Communication
5.00
adam rowe
CEO at Sakscom
reviewed on 2/8/2024
Attention to detail
Their attention to detail and commitment to accuracy have significantly improved our financial management. The team is professional, responsive, and always ready to assist with any queries. Their expertise has streamlined our bookkeeping processes, making it easier for us to focus on our core business operations. We highly recommend Ledger Labs to anyone in need of reliable and efficient bookkeeping services.
Budget
5.00
Schedule
5.00
Quality
5.00
Communication
5.00
john holland
Manager at PlusSend
reviewed on 23/7/2024
Timely and Reliable Delivery

Ledger Labs consistently delivered high-quality work on time, demonstrating their reliability and commitment to meeting deadlines. Their punctuality in delivering reports and updates helped maintain smooth business operations and strategic planning. Their ability to adapt to changing needs and provide flexible solutions was a standout feature. Whether it was adjusting the scope of work or refining financial processes, Ledger Labs showcased a strong commitment to meeting the evolving needs of the business.

Budget
5.00
Schedule
5.00
Quality
5.00
Communication
5.00
Reviews (28)
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

Gary Jain

CFO | IRS Enrolled Agent

Gary started Ledger Labs in 2014 and has helped over 2,000 ecommerce businesses improve their finances. He focuses on CFO services, setting up ERP systems such as NetSuite, Odoo, and QuickBooks, and automating financial processes for growing online brands.

Allison Rinehimer Operations Manager

Allison Rinehimer

Operations Manager

Allison is a Certified Public Accountant (CPA) and a member of the AICPA. She oversees operations at Ledger Labs, ensuring accurate, compliant financials for hundreds of clients. With experience in both public and private accounting, she builds scalable systems that support fast-growing ecommerce businesses.

Matt Hidalgo Accountant

Matt Hidalgo

Accountant

Matt brings 7+ years of accounting experience across ecommerce, SaaS, and technology. He specializes in financial reporting, month-end close management, and ERP implementations (including NetSuite transitions). Matt ensures our clients get accurate, timely financials they can rely on for growth decisions.

Why Sellers Switch to Our Ecommerce Accounting Team

Over 2,000 ecommerce businesses have switched to us from DIY accounting or other ecommerce accounting firms. Here’s the real difference:

FeatureGeneric BookkeeperDIY AccountingLedger Labs
Platform-Synced BookkeepingManual imports with frequent errors and platform mismatchesYou spend 20–30 hours/month downloading CSVs and reconcilingAutomated, daily reconciliation across Shopify, Amazon, Stripe, and PayPal, fully mapped to your chart of accounts
Accurate COGS & Inventory TrackingGeneric cost assumptions with no inventory reconciliation or per-product visibilityYou’re guessing inventory values in spreadsheetsSKU-level COGS tracking with real-time inventory valuation and true landed cost calculation
Multi-Channel Financial ConsolidationDisorganized reporting split between systems and spreadsheetsSeparate spreadsheets per channel, you’re drowning in dataClean consolidation across sales channels with unified reporting and seamless data flow
Sales Tax Compliance & FilingMissed thresholds and late filings due to manual oversight or outdated systemsYou’ll deal with it when audited (hopefully never)Nexus monitoring, accurate sales tax mapping, and timely filing across all states and platforms
Profitability Reporting & SKU AnalysisFlat P&Ls with no breakdowns or actionable visibilityYou know revenue, but not profit by product or channelClear dashboards showing profit margins by SKU, channel, ad campaign, and fulfillment method
Return & Refund TrackingRefunds overlooked or double-counted, distorting revenueManually tracking refunds in separate spreadsheetsFully reconciled returns, chargebacks, and partial refunds are reflected accurately in your financials
Real-Time Cash Flow MonitoringDelayed cash flow statements and a lack of forecast accuracy (45-60 days behind)You're guessing if you can afford that $200K inventory orderDaily insights into cash flow , payouts, liabilities, and working capital across all processors
Audit-Ready Financials & DocumentationVague 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
Ecommerce Specialist AccessSlow turnaround from generalized support teams with limited ecommerce experienceGoogle searches and Reddit forums are your "advisors."Slack/email access to your dedicated ecommerce accountant for fast answers and strategic insight
Monthly Close Timeline30-45 days after month-end (too late to act on data)Never (or quarterly at best when you remember)Financial statements delivered by the 15th of every month, guaranteed
Monthly Cost$500-1,000/month (for basic, often inaccurate work)$0 cash, but 100+ hours of your time/month (worth $10K-20K)Starting at $1,200/month for comprehensive ecommerce accounting services
Setup & Onboarding Time8-12 weeks (if they understand ecommerce at all)Ongoing chaos with no clear system2-4 weeks to full platform integration and historical cleanup

Platform-Synced Bookkeeping

Generic Bookkeeping
Manual imports with frequent errors and platform mismatches
DIY Accounting
You spend 20–30 hours/month downloading CSVs and reconciling
Ledger Labs
Automated, daily reconciliation across Shopify, Amazon, Stripe, and PayPal, fully mapped to your chart of accounts
Generic Bookkeeping

Generic cost assumptions with no inventory reconciliation or per-product visibility

DIY Accounting

You’re guessing inventory values in spreadsheets

Ledger Labs

SKU-level COGS tracking with real-time inventory valuation and true landed cost calculation

Generic Bookkeeping
Disorganized reporting split between systems and spreadsheets
DIY Accounting
Separate spreadsheets per channel, you’re drowning in data
Ledger Labs
Clean consolidation across sales channels with unified reporting and seamless data flow
Generic Bookkeeping
Missed thresholds and late filings due to manual oversight or outdated systems
DIY Accounting
You’ll deal with it when audited (hopefully never)
Ledger Labs
Nexus monitoring, accurate sales tax mapping, and timely filing across all states and platforms
Generic Bookkeeping
Flat P&Ls with no breakdowns or actionable visibility
DIY Accounting
You know revenue, but not profit by product or channel
Ledger Labs
Clear dashboards showing profit margins by SKU, channel, ad campaign, and fulfillment method
Generic Bookkeeping
Refunds overlooked or double-counted, distorting revenue
DIY Accounting
Manually tracking refunds in separate spreadsheets
Ledger Labs
Fully reconciled returns, chargebacks, and partial refunds are reflected accurately in your financials
Generic Bookkeeping
Delayed cash flow statements and a lack of forecast accuracy (45-60 days behind)
DIY Accounting
You’re guessing if you can afford that $200K inventory order
Ledger Labs

Daily insights into cash flow , payouts, liabilities, and working capital across all processors

Generic Bookkeeping
Vague notes, missing context, and last-minute
DIY Accounting
“I’ll figure it out at tax time” (famous last words)
Ledger Labs
Well-organized, documented entries with supporting detail for every
Generic Bookkeeping
Slow turnaround from generalized support teams with limited ecommerce experience
DIY Accounting
Google searches and Reddit forums are your “advisors.”
Ledger Labs
Slack/email access to your dedicated ecommerce accountant for fast answers and strategic insight
Generic Bookkeeping
30-45 days after month-end (too late to act on data)
DIY Accounting
Never (or quarterly at best when you remember)
Ledger Labs
Financial statements delivered by the 15th of every month, guaranteed
Generic Bookkeeping
$500-1,000/month (for basic, often inaccurate work)
DIY Accounting
$0 cash, but 100+ hours of your time/month (worth $10K-20K)
Ledger Labs
Starting at $1,200/month for comprehensive ecommerce accounting services
Generic Bookkeeping
8-12 weeks (if they understand ecommerce at all)
DIY Accounting
Ongoing chaos with no clear system
Ledger Labs
2-4 weeks to full platform integration and historical cleanup

Accounting Software We Work In

Our Testimonials

Hear from More Business Owners Who Were in Your Exact Position

Find out what our customers are saying about our services.

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

Our P&L said we were profitable, but the cash never showed up. Turns out our old bookkeeper was expensing inventory when we bought it, not when it sold. Ledger Labs fixed our COGS and inventory accounting, and the real picture was very different. Now I finally know our true margins.

Bianca Fontaine CEO

Sales tax was my nightmare; I had no idea I'd triggered nexus in eight states until Ledger Labs flagged it. They registered us, set the platforms to collect correctly, and got us filing on time. They caught a liability that could've turned into a five-figure problem at audit.

Devin Ashworth Owner

We were scaling revenue, but our profit wasn't moving, and I couldn't figure out why. Ledger Labs broke down margin by SKU after fees, shipping, and ad spend, and two of our 'bestsellers' were actually losing money. We cut them, and our bottom line jumped.

Harmony Liang Co-Founder
FAQ

Ecommerce Accounting Questions We Get A Lot

1. What ecommerce platforms do you work with?
All major platforms, Amazon (FBA & FBM), Shopify, Walmart, Etsy, eBay, TikTok Shop, BigCommerce, and any channel you sell on. We also integrate with payment processors like Stripe, PayPal, Square, and Shopify Payments.
Our bookkeeping runs on a fixed monthly schedule, so you get the same reports on the same date every month:
  • Days 1–5 – 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.
  • Days 6–10 – 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.
  • Days 11–15 – Financial Reporting: we deliver your P&L, balance sheet, cash flow statement, and SKU-level margin report by the 15th, with a summary of what changed.
We monitor your nexus footprint across all 50 states, register you where needed, configure your platforms to collect correctly, and file returns on time, proactively tracking threshold changes so you stay compliant and avoid penalties.
Yes, we provide 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.
Yes, we track inventory as an asset, calculate accurate COGS including landed costs (shipping, duties, freight), and provide real-time inventory valuation. We also integrate with inventory systems like Finale, Inflow, and SkuVault.
We work 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.
We integrate directly with your sales channels, payment processors, inventory systems, and ad platforms using tools like A2X, Link My Books, and native APIs, so everything syncs automatically, with no manual data entry.
You get direct access to your 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.
Two to four weeks, depending on complexity. We integrate your sales channels, clean up historical data if needed, set up a proper chart of accounts, and deliver your first monthly financials.
Yes. As a CPA and IRS Enrolled Agent–led team, we prepare business returns (Form 1120, 1120S, 1065, Schedule C) and maximize ecommerce-specific deductions. Because we manage your books year-round, tax season is seamless, not chaotic.

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

Empowering Business Confidence Through Precision and Insight

business consultation

Navigating Financial Complexity to Secure Investment

finance operation

Revolutionizing Finance Operations to Unlock Efficiency and Personal Freedom

We value your privacy

We use cookies to enhance your experience and analyse traffic. Privacy Policy

Get Ready-to-use Templates for Financial Statements