E-commerce accountant, CPA or bookkeeper: which one does your store need?

By Sam’s List team · Updated November 2026

Short answer: Most online sellers need two kinds of help. A bookkeeper or e-commerce accounting firm keeps the monthly books: reconciling marketplace payouts, tracking inventory and cost of goods, and producing margin reports. A CPA or tax professional prepares income tax returns and advises on tax planning and entity choice. Some firms do both; many specialize in one. Ask each firm which it does.

Who does what

RoleTypical workHire when
E-commerce bookkeeper or accounting firmPayout reconciliation, inventory and COGS, monthly close, P&L by channelBooks are behind, or you cannot see margin by product or channel
Controller-level accountantAccrual close, inventory accounting, reporting for lenders or investorsRevenue and inventory have grown, or a lender asks for statements
CPA or enrolled agentIncome tax returns, IRS noticesEvery year, at a minimum
Tax strategist or tax-planning CPAPlanning ahead of year-end, entity choice, multi-state questionsProfits are growing and you want to plan, not just file

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Bookkeeping and accounting for your store

Ottit focuses on bookkeeping and controllership for e-commerce, SaaS and SMB operators. For income tax returns and tax planning, work with a CPA or tax professional.

Tax planning for your store

CPA on Fire is a tax advisory firm on Sam’s List:

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CPA on Fire

CPA on Fire is a concierge-level tax advisory firm led by former Big Four accountants, delivering proactive, forward-thinking strategies that go far beyond traditional accounting to support the growth and success of ambitious business owners & founders.

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Questions to ask before you hire

See e-commerce bookkeeping cost, Amazon seller accounting and S corps for e-commerce sellers. Browse e-commerce accountants and tax planning.

Frequently asked questions

Do I need a CPA or a bookkeeper for my online store?

Usually both: a bookkeeper or accounting firm for the monthly books, and a CPA or tax professional for tax returns and planning. Some firms offer both.

What does an e-commerce accountant do?

Reconciles marketplace and processor payouts, tracks inventory and cost of goods, closes the books monthly and reports margin by product or channel.

What is a tax strategist?

Usually a CPA or tax professional focused on planning ahead of year-end rather than only preparing returns.

What should I ask an e-commerce accountant?

Which channels and tools they know, whether they do books, tax or both, cash vs accrual, inventory method, report timing and how they coordinate with your tax preparer.

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Related on Sam’s List

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