For a store that sells on Shopify or Amazon, the best setup is a settlement connector, A2X or Link My Books, feeding a general ledger such as QuickBooks Online or Xero, because the connector is what turns one net deposit back into sales, fees and refunds. A seller who is still forming the business should start one step earlier: entity, EIN and a separate business account first, with ZenBusiness Money Pro at $30 per month (as of 2026-10-06) as a way to have bookkeeping handled for you. For payout reconciliation at volume, though, a ledger plus a connector is the stronger fit.
What goes wrong when a payout is treated as revenue?
A payout is not a sale. Shopify Payments, Amazon and similar platforms collect the customer's money, subtract their fees, subtract refunds and any held-back reserves, and deposit the net amount. That deposit rarely matches any single order.
If the bank feed is categorised as "sales", several things break at once. Revenue is understated by the fees and refunds netted out of it. Fees never appear as an expense, so profit looks higher than it is. And the totals never agree with the platform's own sales report, which makes every month-end reconciliation a hunt for small differences.
A reserve adds a further wrinkle. Money held back is not lost income, but it is not in the bank yet either, so it needs to sit as a balance owed to the seller until it is released. The correct treatment is to record gross sales, fees, refunds and adjustments as separate lines, then match the net total to the deposit.
How does a settlement connector fix this?
A connector reads each payout or settlement, splits it into its components, and posts a summary entry to the ledger. The summary equals the deposit, so the bank line reconciles in a single match. The same split is possible by hand: export the settlement report, build a journal entry, and post it.
By-hand works for a handful of payouts a month from one channel. It stops working with daily Shopify payouts, twice-monthly Amazon settlements and a second or third channel. Whether a given ledger or service handles payouts natively is not something this page can confirm from published sources, so check each vendor's documentation.
Which tools handle payout reconciliation?
The tools 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, not a ledger, so it needs QuickBooks Online or Xero underneath it. It starts at $29 per month per sales channel, with Walmart from $79 per month. A store on both Shopify and Amazon should expect to pay for two channels. It suits sellers who want payout summaries posted automatically to a standard ledger.
Bench
Bench is a bookkeeping service rather than software. Bookkeeping Light 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. Whether a 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 in this comparison, aimed at online sellers. It is priced by order volume and channel count through a calculator, with no flat published tier, so no figure can be quoted here. That is worth knowing when comparing it with a connector that lists a starting price. It suits sellers who would rather price their own volume than accept a per-channel rate.
QuickBooks Online
QuickBooks Online has a Free plan at $0, then Simple Start at $38 per month, Essentials at $85, Plus at $140 and Advanced at $340. The 50% offer for 3 months is promotional and not the ongoing price. It is the most common ledger and easy to hand to an accountant. For payouts, it is the usual partner for a connector.
Wave
Wave's Starter plan is free, and Pro is $19 per month or $190 per year. The introductory rate of $9.50 per month for 3 months on Pro 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, with the caveat that no payout-level reconciliation for Shopify or Amazon is documented here.
Xero
Xero's plans are Early at $27 per month, Growing at $59 per month and Established at $97 per month. The 80% discount for 3 months is promotional and not the ongoing price. It is a strong ledger for sellers who prefer its layout, and like QuickBooks Online it is typically paired with a connector for marketplace payouts.
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, Premium at $70, Elite at $150 and Ultimate at $275. It suits sellers who want a lower-priced ledger and are willing to verify how its sales integrations treat payouts.
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. Whether it reconciles marketplace payouts is not published, so that is a question to ask directly.
How do the options compare?
Providers are listed alphabetically, not by preference. Figures are monthly as of 2026-10-06.
| Provider | Type | Published starting price | Payout role |
|---|---|---|---|
| A2X | Settlement connector | $29 per channel | Splits payouts into ledger entries |
| Bench | Bookkeeping service | $199 | Not published |
| Link My Books | Settlement connector | Not published | Splits payouts into ledger entries |
| QuickBooks Online | Ledger | $0 (Free), $38 (Simple Start) | Ledger for a connector |
| Wave | Ledger | $0 (Starter) | Not published |
| Xero | Ledger | $27 | Ledger for a connector |
| ZenBusiness Money Pro | Bookkeeping service | $30 | Not published |
| Zoho Books | Ledger | $0 (Free), $20 (Standard) | Not published |
Which records should be kept alongside the payout reports?
A clean reconciliation is only useful if the underlying records are kept for as long as the rules require. The Internal Revenue Service sets the general period at 3 years. That applies unless one of three exceptions does: under-reporting income by more than 25% of the gross income shown on the return (6 years), not filing a return at all (indefinitely), or filing a fraudulent return (indefinitely).
The same IRS guidance gives 7 years for a claim for a loss from worthless securities or a bad debt deduction, and at least 4 years for employment tax records, counted from the later of the date the tax becomes due or is paid.
IRS Publication 583 lists the documents that support 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. A marketplace settlement report is not named on those lists, so keeping the matching bank deposit slips and invoices with it is the safer approach.
For sellers with employees, the U.S. Department of Labor's Fact Sheet 21 says employers must preserve payroll records, collective bargaining agreements, and sales and purchase records for at least three years, with time cards and wage-related supporting records kept for 2 years. On sales tax, the California Department of Tax and Fee Administration's Publication 116 says to keep records at least 4 years, and through the end of any audit. Other states are not covered here.
Why does a separate business account matter for reconciliation?
A payout reconciles only if it lands somewhere the books can match it. Publication 583 says one of the first things to do when starting a business is open a business checking account and keep it separate from the personal one. It adds that the account should be used for business purposes only, with the source of deposits and the type of expense indicated.
A seller who has not yet formed an entity or separated accounts should fix that before choosing a connector. ZenBusiness handles the entity and EIN steps and offers a free accounting consultation to customers who form with it. It no longer offers business banking, so the account itself has to come from a bank. Once that is in place, the payout tools above have something clean to reconcile against.
How should a seller choose?
Count the payouts and the channels first. One channel with a few payouts a month can be handled by hand on a free or low-cost ledger. Several channels with frequent payouts justify a connector, and the cost is measured against the hours spent building journal entries.
Then decide who does the work. An owner who will keep the books pairs a ledger with a connector. An owner who wants to hand it off looks at a service such as Bench or ZenBusiness Money Pro, after confirming how payouts are handled.
Finally, budget on ongoing prices. QuickBooks Online, Wave and Xero all lead with a 3-month discount, and the plan prices above are the figures that matter after it ends.
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.