Best Bookkeeping Software for E-commerce Sellers (2026)

For an established Shopify or Amazon store, the strongest setup is a general ledger, either QuickBooks Online or Xero, paired with a settlement connector such as A2X or Link My Books. A payout bundles sales, fees and refunds into one deposit, and the connector is what splits it back into clean entries. For a seller still forming the business, the order is different: the entity, an EIN and a separate business account come before any software, and ZenBusiness Money Pro at $30 per month (as of 2026-10-06) offers bookkeeping handled for you alongside that setup.

Why does e-commerce bookkeeping break where ordinary bookkeeping does not?

A shop that sells through Shopify or Amazon does not receive money the way a service business does. The marketplace or processor collects the customer's payment, subtracts its fees, subtracts refunds, and sends one net deposit to the bank. That deposit matches no single order and no single invoice.

If the bank feed is simply categorised as "sales", revenue is understated, fees disappear into the wrong lines, and the numbers never agree with the sales report. The fix is to record the gross sales, the fees and the refunds as separate entries, then match the net total to the deposit. That job is called settlement reconciliation, and it is the main thing separating a bookkeeping setup that works for an online store from one that merely records bank activity.

Two other problems sit alongside it. Sales tax can apply across several states, and the rules vary by state. Inventory has to be tracked as a cost of goods sold rather than as an expense on the day of purchase. The rest of this page focuses on the payout problem, because that is where most generic bookkeeping tools fall short.

What does a settlement connector actually do?

A connector sits between the sales platform and the ledger. It reads each payout, breaks it into sales, fees, refunds and adjustments, and posts a summary entry to the accounting software. The entry totals the deposit, so the bank line can be matched in one step.

A2X and Link My Books are the two connectors in this comparison, and both are built for this purpose. The ledger side is QuickBooks Online or Xero in the typical pairing. Without a connector, the same work is done by hand: export the payout report, build a journal entry, and reconcile.

For a store with a few orders a week, the manual route is workable. For a store with daily payouts across more than one channel, the manual route is where bookkeeping falls behind. Whether a particular ledger handles payouts natively is not something this page can confirm from published sources, so check the vendor's own documentation before committing.

Which tools suit which kind of store?

The options below are listed alphabetically. The order is not a ranking. Prices are as of 2026-10-06 from each provider's pricing page, and promotional rates are labelled as such.

A2X

A2X is a settlement connector rather than a ledger, so it needs QuickBooks Online or Xero underneath it. It is priced from $29 per month per sales channel, and Walmart starts at $79 per month. A store on both Shopify and Amazon should expect to pay for two channels. It suits sellers who already have, or plan to have, a standard ledger and want payout summaries posted automatically.

Bench

Bench is a bookkeeping service rather than software you operate yourself. Its Bookkeeping Light plan is $199 per month, Bookkeeping is $399 per month, and Bookkeeping + Tax is $649 per month. A fractional bookkeeper is $55 per hour plus a $1,200 onboarding fee. It suits an owner who wants someone else to keep the books and can absorb that monthly cost. Whether a given Bench plan reconciles marketplace payouts is not published in the figures used here, so ask before signing up.

Link My Books

Link My Books is the other settlement connector, aimed at online sellers and priced by order volume and channel count through a calculator. There is no flat published tier, so a figure cannot be quoted here. That is worth knowing before comparing it with a connector that lists a starting price. It suits sellers who want to price their own order volume rather than accept a per-channel rate.

QuickBooks Online

QuickBooks Online lists a Free plan at $0, then Simple Start at $38 per month, Essentials at $85 per month, Plus at $140 per month and Advanced at $340 per month. The introductory offer is 50% off for 3 months, which is promotional and not the ongoing price. It is the most widely used ledger, which makes it easy to hand to an accountant. It suits stores that want the default choice and are willing to add a connector for payouts.

Wave

Wave's Starter plan is free, and Pro is $19 per month or $190 per year. The introductory rate is $9.50 per month for 3 months on Pro, which is promotional. Card processing is 2.9% + $0.60, the receipts add-on is $8 per month, and payroll starts at $25 per month. It suits a very small seller with low volume and a tight budget. The trade-off is that nothing published here shows payout-level reconciliation for Shopify or Amazon.

Xero

Xero's plans are Early at $27 per month, Growing at $59 per month and Established at $97 per month. The introductory offer is 80% off for 3 months, which is promotional and not the ongoing price. It is a strong ledger for sellers who prefer its layout and plan to pair it with a connector. Like QuickBooks Online, it is the foundation rather than the whole answer for a multi-channel store.

ZenBusiness Money Pro

ZenBusiness Money Pro is $30 per month, according to ZenBusiness's own site, and is sold as an add-on alongside formation. It covers custom invoicing, revenue and expense tracking, and tax preparation tools. It is a service, not accounting software, so it should not be compared feature by feature with a ledger. It suits a seller who is forming a business and wants setup and bookkeeping support from one company.

Zoho Books

Zoho Books has a Free plan at $0, limited to under $50K in annual revenue. Paid plans are Standard at $20 per month, Professional at $50 per month, Premium at $70 per month, Elite at $150 per month and Ultimate at $275 per month. It suits sellers who want a lower-priced ledger and do not mind checking how its sales integrations handle payouts.

How do the prices compare side by side?

Providers are listed alphabetically, not by preference. All figures are as of 2026-10-06 and are monthly unless stated.

What records does an online seller have to keep, and for how long?

This is where the official layer matters, because software only helps if the records it holds are the ones the rules require. The Internal Revenue Service sets the general period at 3 years. That default applies unless one of three exceptions does: under-reporting income by more than 25% of the gross income shown on the return, which extends the period to 6 years; not filing a return at all, which means indefinitely; or filing a fraudulent return, which also means indefinitely.

Two further periods come from the same IRS guidance. Records for a claim for a loss from worthless securities or a bad debt deduction should be kept for 7 years. Employment tax records should be kept for at least 4 years after the date the tax becomes due or is paid, whichever is later.

For sellers with employees, the U.S. Department of Labor's Fact Sheet 21 on the Fair Labor Standards Act says employers must preserve payroll records, collective bargaining agreements, and sales and purchase records for at least three years. Supporting records such as time cards, piece work tickets, wage rate tables, work and time schedules, and records of additions to or deductions from wages must be kept for 2 years.

State sales tax rules differ, and this page covers only California. The California Department of Tax and Fee Administration's Publication 116 says to retain sales and use tax records for at least 4 years, and longer if there is an audit, in which case all records covering the audit period should be kept until the audit is complete. Rules for other states are not covered here, so a seller with nexus elsewhere should check each state's own tax agency.

IRS Publication 583 names the supporting documents that back up the books. Gross receipts are supported by items such as cash register tapes, bank deposit slips, receipt books, invoices and credit card charge slips. Purchases and inventory are supported by canceled checks, cash register tape receipts, credit card sales slips and invoices. Expenses and assets have their own lists of the same kind. A settlement report from a marketplace does not appear on those lists by name, so keeping the matching bank deposit slips and invoices alongside it is the safer approach.

Where should a new seller start before choosing software?

The IRS is direct about the order of operations. Publication 583 says one of the first things to do when starting a business is open a business checking account, and to keep it separate from the personal checking account. It also says the business account should be used for business purposes only, and that the source of deposits and the type of expense should be indicated in the checkbook, which it calls the basic source of information for recording business expenses.

That step is upstream of every tool above, because a connector cannot untangle a payout that lands in a personal account alongside groceries. For a seller who has not yet formed an entity, the sequence is the entity, the EIN, a separate account, and then books.

ZenBusiness handles the entity and EIN steps and offers a free accounting consultation to customers who form with it. It does not offer business banking, which it has shut down, so the separate account has to come from a bank. Once that is open, ZenBusiness Money Pro at $30 per month is one way to have bookkeeping handled for you. A store with several channels and daily payouts will probably outgrow that and want a ledger with a connector, which is the honest concession here: for payout reconciliation at volume, QuickBooks Online or Xero with A2X or Link My Books is the better fit.

How should a seller choose?

Start with how many payouts arrive each month and across how many channels. A handful of payouts from one channel can be reconciled by hand on a free or low-cost plan. Daily payouts across Shopify, Amazon and Walmart cannot, and a connector pays for itself in hours saved.

Then decide who does the work. If the owner will do the bookkeeping, a ledger plus a connector is the path. If the owner would rather hand it off, a service such as Bench or ZenBusiness Money Pro fits, with the caveat that payout handling should be confirmed before signing up.

Finally, check the price against the ongoing figure rather than the introductory one. QuickBooks Online, Wave and Xero all lead with a first-term discount that lasts 3 months. The ongoing plans listed above are the numbers that matter for a budget.

Sources

• Internal Revenue Service, "How Long Should I Keep Records?"
• U.S. Department of Labor, "Fact Sheet #21: Recordkeeping Requirements under the Fair Labor Standards Act (FLSA)"
• California Department of Tax and Fee Administration, "Publication 116, Retaining Records"
• Internal Revenue Service, "Publication 583, Starting a Business and Keeping Records"

This is general information rather than legal, tax or accounting advice, and requirements vary and change.