As your ecommerce business grows, your finances can slowly become a nightmare. You’re reconciling Amazon payouts, sorting through Shopify fees…and now the math doesn’t quite add up.
Relate? Perhaps it’s time to hire a virtual bookkeeper.
If you’re considering working with one but don’t know where to start, this guide is for you.
We’ll cover what a bookkeeper does, what it costs, how to hire the right one, and why ecommerce businesses need specialized help.
What Is a Virtual Bookkeeper?
A virtual bookkeeper is someone who uses cloud-based bookkeeping software to manage your books remotely.
And just because they’re “virtual” or remote doesn’t mean they provide a reduced level of service. A reliable one brings the same professional judgment as an in-house hire. They catch errors, categorize transactions correctly, and give you numbers you can trust.
Also, an online bookkeeper is not the same as accounting software. QuickBooks won’t tell you that your Amazon payouts are miscategorized. A real person will.
This is the foundation of what we call ecommerce bookkeeping. Keeping your books accurate month after month so you always know where you stand.
What Does a Virtual Bookkeeper Do for Your Business?
Here’s what a bookkeeper virtual assistant’s day-to-day scope of work looks like:
- Recording and categorizing transactions across all accounts and payment processors.
- Reconciling bank accounts to make sure your books match your bank balances.
- Tracking the cost of goods sold (COGS) and inventory adjustments so your profitability numbers are real.
- Generating monthly financial statements (P&L, balance sheet, and cash flow statement).
- Coordinating with your CPA for tax planning and filing.
- Updating your chart of accounts as your business evolves.
Each month, you should get the following deliverables from your bookkeeper:
Why Do Ecommerce Businesses Need a Virtual Bookkeeper?
Most accounting guides don’t tell you that ecommerce accounting is more complex than almost any other type of accounting.
A standard service typically has only one revenue stream and a handful of expense categories. Ecommerce sellers, however, have multiple platforms, dozens of fee types, and inventory that changes daily.
Here are specific complexities that ecommerce sellers deal with that a generic virtual assistant for small businesses often handles incorrectly:
- Multi-channel sales: Amazon, Shopify, Etsy, eBay, and Walmart each generate payouts that need to be categorized separately, rather than lumped together.
- Payout reconciliation: Stripe and PayPal deposits do not equal gross revenue. Fees, refunds, and adjustments are all included in seller platform deposits.
- Sales tax nexus: Economic nexus thresholds now apply in most states. According to the Sales Tax Institute, most states have a threshold of $100,000 in sales or 200 transactions.
- COGS accuracy: Your cost of goods sold has to be tied to your actual inventory. If it’s not tracked correctly, your P&L is unreliable.
Virtual Bookkeeper vs. In-House Bookkeeper vs. Accounting Software
When you decide to hire a bookkeeper, you have three options: go virtual, hire in-house, or use software and manage it yourself. Each suits a different stage of business growth.
Here’s a clear breakdown:
Virtual Bookkeeping Services Pricing – What to Budget
There are three factors that affect pricing: your monthly transaction volume, the number of sales channels you’re on, and whether catch-up or clean-up work is needed before ongoing bookkeeping can start.
You’ll encounter these pricing structures when talking to providers:
- Monthly retainer: For ongoing virtual bookkeeping, where you pay a flat fee each month.
- Hourly: Applies to ad hoc support, audits, or one-off projects.
- Project-based: For one-time clean-up or catch-up work if your books are behind.
Use this guide when setting a budget for the specific engagement type you’re looking for:
Note that ecommerce businesses typically pay more than a general small business because the work is more complex. Factors that drive pricing up include inventory tracking requirements and whether taxes are bundled in.
If you want a specific quote based on your business, you can check our pricing.
What to Look for in a Virtual Bookkeeper
Already have a provider in mind? Here’s what to look for before you sign anything:
Ecommerce-Specific Experience to Require
The right virtual bookkeeper isn’t just someone who knows how to do the books. They’re someone who knows ecommerce bookkeeping.
Before you hire, confirm that they have experience in:
- The specific platforms you sell on
- Tools like A2X or LinkMyBooks for automating payout reconciliation
- Correctly categorizing Amazon payouts
- Inventory-based tracking
- Multi-state tax obligations and nexus thresholds
A generalist who lacks these competencies will produce books that look clean on the surface but contain systematic errors in COGS and revenue classification. The right place to look for specialized ecommerce accounting services is a provider built specifically for online sellers.
Questions to Ask Before You Hire
Ask these questions in your discovery call. The answers will tell you whether they’re the right fit.
- What ecommerce platforms do you have direct bookkeeping experience in? Amazon and Shopify are the bare minimum. Ask about Walmart, eBay, and Etsy, too.
- How do you handle Shopify or Amazon payouts? The right answer: They reconcile the payout to gross sales, fees, and refunds, not just record the deposit.)
- What accounting software do you use, and do I get access to my books? If they use a proprietary system that locks you out? Major red flag.
- How do you handle catch-up work if my books are behind? Look for providers who offer catch-up bookkeeping as a service. Not every bookkeeper handles it.
- What does your monthly communication cadence look like? You should know when to expect your reports and how to reach someone if you have questions.
Best Virtual Bookkeeper Services to Choose From
Not all virtual bookkeeping services are built the same. Most are designed for generic small businesses.
Here are five worth looking at, including who each one is best for:
1. EcomBalance
Top pick for ecommerce sellers. Our service is built by ecommerce sellers for ecommerce sellers. Founders Nathan Hirsch and Connor Gillivan grew an Amazon business to $25M+ in sales before building EcomBalance. They designed their bookkeeping service with a seller-first perspective.
Who it’s for: Amazon, Shopify, Walmart, eBay, and Etsy sellers who want ecommerce-specific bookkeeping.
Key features:
- Monthly books delivered by the 15th
- Financial reports with analysis
- Dedicated bookkeeper and team
- Integration with all major sales channels into QuickBooks or Xero
- CPA coordination and tax services available under the same roof
- First month of bookkeeping free
Limitation: Focused on ecommerce bookkeeping.
Ready to get your books handled by people who actually understand ecommerce?
Start with EcomBalance’s free first month, and see what it looks like to have clean books delivered every month.
2. QuickBooks Live
This is Intuit’s built-in bookkeeping add-on for QuickBooks Online users. If you’re already using QBO, this is a frictionless option.
Who it’s for: Small businesses already inside the QuickBooks ecosystem looking for basic bookkeeping support.
Key features:
- Bookkeepers matched through Intuit
- Works entirely inside QuickBooks Online
- Monthly clean-up and reconciliation
Limitation: Generalist service with no ecommerce-specific methodology.
3. Pilot
Tech-forward bookkeeping service built for startups and venture-backed companies.
Who it’s for: Startups and VC-backed businesses that need accrual-basis bookkeeping with controller oversight and CFO-level support.
Key features:
- Dedicated finance expert
- Accrual-basis bookkeeping
- Financial statements delivered monthly
- Works inside QuickBooks Online
- Optional CFO and tax support
Limitation: Pricing scales with monthly expenses, and can climb quickly for higher-revenue businesses.
4. Bookkeeper360
Full-service accounting platform that offers payroll, tax, and CFO advisory.
Who it’s for: Growing businesses that need advisory services on top of bookkeeping.
Key features:
- Compatible with QuickBooks and Xero
- CFO advisory add-on
- Payroll and tax services available
- Dedicated accountant
Limitation: Less ecommerce-specific depth than a specialized provider.
5. Upwork (Freelance Virtual Bookkeepers)
This is a freelance marketplace where you can hire individual bookkeepers for hourly or project-based engagements.
Who it’s for: Early-stage sellers with low transaction volume and tight budgets.
Key features:
- Large talent pool
- Flexible hour and project-based arrangements
- Wide range of software experience
Limitation: Vetting is entirely on you. Quality also varies significantly, and finding someone with real ecommerce experience takes time.
Tools Your Virtual Bookkeeper Should Use
The tools a virtual bookkeeper uses directly affect the accuracy and efficiency of their work.
Your pick should be working with tools from each of these four categories:
QuickBooks Online is the most widely used platform for virtual bookkeeping. Xero is the main alternative, particularly for businesses with international sales or multi-currency needs.
If you encounter a bookkeeper who’s unwilling to work in your chosen software, or who uses proprietary software that limits access to your own financial data (Remember what happened to Botkeeper?), take that red flag seriously.
Frequently Asked Questions (FAQs)
Here are answers to the most common questions ecommerce business owners ask about virtual bookkeeping:
What is the Difference Between a Virtual Bookkeeper and an Accountant?
A bookkeeper records and analyzes your transactions monthly.
An accountant analyzes those records, handles tax strategy, and files your taxes. Most ecommerce businesses need both.
What Financial Reports Should a Virtual Bookkeeper Deliver Each Month?
At a minimum, you should get a P&L Statement, Balance Sheet, Cash Flow Statement, and a reconciliation summary for each sales channel.
If your bookkeeper doesn’t deliver all of these, that’s a problem.
Is QuickBooks Online Required to Work with a Virtual Bookkeeper?
It’s the most common platform, and most services support it, with Xero as the main alternative for businesses with international sales.
Either way, avoid bookkeepers who use proprietary systems that restrict access to your own financial data.
Can a Virtual Bookkeeper Handle Multiple Ecommerce Sales Channels?
Yes, but only if they have direct experience with multi-channel reconciliation and tools like A2X or LinkMyBooks.
A generalist without that experience will miscategorize payouts and produce inaccurate books.
What Are the Biggest Red Flags When You Hire a Virtual Bookkeeper?
The biggest red flags are:
- Having no ecommerce platform experience.
- Inability to explain how they handle Amazon or Shopify payouts.
- Proprietary software that locks you out of your books.
- No clear monthly delivery schedule.
Walk away if you see any one of these.
Conclusion
A virtual bookkeeper is the right hire for businesses that have outgrown DIY bookkeeping but aren’t yet at the scale that justifies a full-time in-house hire.
If you’re an ecommerce seller, the differentiating factor to look for is always an ecommerce-specific experience and methodology.
A bookkeeper who understands multi-channel payouts, COGS tracking, and platform fee categorization is the one who’s equipped to give you financial statements you can actually use to run your business.
If you’re ready to work with a team built specifically for ecommerce sellers, ecommerce bookkeeping is what we do every day at EcomBalance.
