Help & user guide

Getting started

FreeAgent included with some UK banks
If you bank with Mettle, NatWest Business or RBS Business, FreeAgent is included free. No separate subscription needed. Check if you qualify →

Setup takes about five minutes. Follow the checklist on your Dashboard. It guides you through each step in order.

1
Connect eBay
Dashboard → step 1 → Connect eBay. You'll be redirected to eBay's OAuth page to authorise read access to your Managed Payments account. We never see your password.
2
Connect FreeAgent
Dashboard → step 2 → Connect FreeAgent. Same OAuth flow — FreeAgent issues us a token so we can create invoices and bills on your behalf.
3
Choose the FreeAgent account we import eBay into
Step 3: select the FreeAgent bank account where eBay activity will be posted. Most sellers create one called 'eBay UK seller Account' in FreeAgent Banking → Add account.
4
Choose transaction categories
Step 4: pick which FreeAgent categories sales, fees, postage and promoted listings land in. System defaults match your existing FreeAgent chart of accounts — most sellers just hit 'Use defaults'. You can change them later in Settings.
5
Enable auto-sync
Step 5 → click Set up. If you're on cash basis, first choose how income is dated — payout date (recommended, matches bank deposits) or sale date. Then pick your start date — Latest payout gives the cleanest opening; This tax year / Last tax year let you cover a full tax year. Click Activate auto-sync.
Need to create the eBay bank account in FreeAgent first?
In FreeAgent go to Banking → Add a bank account → Manual account and call it "eBay UK seller Account". Then come back to step 3. FreeAgent's eBay guide
Connecting Etsy instead of eBay?
The five steps above apply the same way — step 1 takes you to Etsy's own sign-in instead of eBay's, and in step 3 you'd name the FreeAgent account "Etsy UK Seller Account" rather than the eBay one. One real difference: Etsy currently posts income on the sale date only — payout-date posting isn't built for Etsy yet, so that choice won't be offered in step 5. Etsy support is newer than eBay's here and hasn't yet been proven against a real trading shop the way eBay has, so if anything looks off, use the chat widget in the bottom-right — that gets to us fastest.

How auto-sync works

Every night, TransactionMerge pulls the previous day's eBay activity, groups it by type, and posts invoices, bills, and credit notes to FreeAgent.

Type
eBay activity
Appears in FreeAgent as
SaleOrder sale proceedsLine on daily invoice → Sales category · auto-explained ✓
FeeFinal value fee, listing feeLine on daily fees bill → eBay Fees category · auto-explained ✓
PostagePostage label chargeLine on daily fees bill → Postage category · auto-explained ✓
PromotedPromoted Listings feeLine on daily fees bill → Advertising category · auto-explained ✓
Fee refundeBay reverses a fee (e.g. cancelled order)Credit line on fees bill · auto-explained ✓
RefundRefund for orderDaily credit note → Sales category · auto-explained ✓
AdjustmentDispute outcome, eBay credit, balance changeSales adjustment · groups under Refunds · auto-explained ✓
PayoutPayout to bank accountBank transfer · auto-explained both sides ✓
OtherLoan repayment, withdrawalBank entry on eBay account · explain manually in FreeAgent
Sync history shows a live breakdown
On the Activity page, click any sync row to expand it. At the top you'll see summary chips — Sales, Refunds, Fees, Transfers, and Funds in transit— each totalling that group for the range (in payout-date mode the chips always net to £0, since each payout's income, fees and transfer cancel out). Below them, the individual FreeAgent entries are listed, grouped by payout, each with a direct link to its document and a ✓ once it's reconciled.

Cash vs accrual accounting

TransactionMerge's two-account model works for both accounting methods. This follows FreeAgent's recommended approach for eBay sellers .

How it works: two accounts in FreeAgent
  1. eBay Account (tracking): TransactionMerge posts daily sales, fees, refunds, and the auto-created payout debit here
  2. Main Bank Account (real bank e.g. Mettle): payout deposits arrive via bank feed and are auto-explained as transfers from your eBay Account
eBay Account (FreeAgent)
├── +£100  Sale           (15 May — transaction date)
├──  –£10  eBay fee       (15 May — transaction date)
└──  –£90  Payout debit   (20 May — auto-created by TransactionMerge)
           Balance: £0

Your main bank account (FreeAgent)
└── +£90  Payout deposit  (21 May — arrives via bank feed)
          Auto-explained as transfer from eBay Account ✓

Cash basis means recording income when the money is available to you. It's the HMRC default for sole traders.

On cash basis you can choose how eBay income is dated. Go to Settings → Sync → Income dating:

  • Sale date (FreeAgent's "Method 2", the default) — income posts when the sale happens. Money in your eBay balance counts as received. Sale on 15 May, payout on 20 May → income on 15 May.
  • Payout date — income posts when the payout actually lands in your bank, so it lines up exactly with your bank deposits. Sale on 15 May, payout lands 20 May → income on 20 May. Sales in a payout are grouped onto that deposit date, and nothing is posted until the money is in your bank.

HMRC accepts either, as long as you use the same method consistently each tax return. Don't switch back and forth. The payout itself is always a zero-impact transfer to your bank. Most UK sole traders use cash basis. If unsure, ask your accountant.

Restoring deleted entries

Don't delete individual invoices, bills, or credit notes from the eBay holding account in FreeAgent. Once deleted, they won't be recreated by the nightly sync — it only moves forward from your last sync, so anything from an earlier date stays gone until it's rebuilt.

Payout transfers are the exception: the nightly sync re-creates a missing transfer for any payout in the last ~45 days. Don't rely on this though — deleting them still risks a mismatch until it settles.

If you've accidentally deleted entries
The nightly auto-sync only covers recent transactions, moving forward from your last sync — entries deleted from an earlier date won't be picked up automatically. Use the chat button in the corner and we'll restore the affected date range for you.

CSV export

All new accounts use the invoice method — your accounting data lives directly in FreeAgent as invoices, bills and credit notes, so there's no separate TransactionMerge export to download. Use FreeAgent's own export tools: Accounting → Reports for P&L, or Banking → [account] → Export for transaction history. FreeAgent export guide

Older statement-method accounts only
If your account still runs on the legacy bank-statement (CSV) sync method rather than the invoice method, each sync row on Activity keeps its own download button, and the by-tax-year export lives in the Export section at the bottom of Reports. New accounts don't use this method, so this won't apply to you.

UK tax year & VAT

Each eBay transaction is dated in FreeAgent based on your income dating setting — either the sale date (when the transaction happened) or the payout date (when eBay paid out to your bank). Either way, FreeAgent's P&L and VAT reports slice correctly by the dates you've chosen. The UK tax year runs 6 April → 5 April.

If you're VAT-registered, VAT is broken out per invoice line in FreeAgent:

  • Sales — default 20%, customisable per listing on the Listings page (e.g. zero-rate books, reduced-rate items, export sales outside the UK)
  • Fees & postage — 20% (eBay charges UK VAT on its own fees regardless of your buyer's location)

FreeAgent's built-in VAT Returns (Taxes → VAT Returns) pull directly from those invoices — no manual totalling needed.

To set per-listing VAT rates: Settings → Sync → Listings & VAT. Unmapped sales are flagged with an amber banner (on the Dashboard and on the Listings & VAT page) so nothing slips through at the wrong rate — map the listing, then click Re-sync right there to update the affected FreeAgent invoices yourself; no need to wait for support. Ranges over 31 days can't be self-served this way — use the chat button instead and we'll run it for you.

Disclaimer
TransactionMerge is a data synchronisation tool. Always verify your VAT calculations with a qualified accountant before filing.

Account & security

Enable 2FA. Go to Settings → Security → Two-factor authentication and scan the QR code with an authenticator app (Google Authenticator, Authy, or 1Password).

You'll receive 10 single-use backup codes. Store them somewhere safe (password manager or printed copy). If you lose your phone, these are the only way back in.

FAQs

Still stuck? . We usually respond quickly.