eBay, Amazon & PayPal Bookkeeping for Accountants: The A2X & LinkMyBooks Alternative
Merchant platforms pay out in lump sums. Inside each payout: sales, fees, refunds, shipping, tax. Breaking those down into proper journal entries is either painful manual work or an expensive subscription. There’s a third option.
At a Glance
| The problem | Merchant platforms deposit lump sums — you need to break them into sales, fees, refunds, and tax for proper bookkeeping |
| Existing tools | A2X ($29–229/mo per channel) and LinkMyBooks (£13–249/mo) — dedicated, effective, separate subscriptions |
| Alternative | CodeIQ Merchant Accounts — built into your existing bookkeeping workflow, not a separate tool |
| Platforms supported | eBay, Amazon, PayPal (CSV upload). Shopify, Etsy not yet supported. |
| Posts to | Xero, QuickBooks, Sage, Pandle |
The lump-sum problem
If you manage clients who sell on eBay, Amazon, or accept payments through PayPal, you already know the pain. These platforms don’t pay out per transaction. They accumulate sales over a settlement period — typically one to two weeks — deduct their fees, subtract refunds, and deposit a single lump sum into your client’s bank account.
That lump sum arrives on the bank statement as something like “EBAY PAYOUT £2,847.31”. Helpful.
What’s actually inside that payout
- Gross sales — the total selling price of items sold during the settlement period
- Final value fees — eBay’s percentage-based commission (typically 10–13%)
- Promoted listing fees — advertising charges if the seller uses eBay’s ad system
- International fees — additional charges on cross-border sales
- Shipping labels — postage purchased through the platform
- Refunds — money returned to buyers, reducing the payout
- Tax withheld — VAT or other taxes collected and remitted by the platform
- Adjustments — disputes, corrections, promotional credits
For accurate bookkeeping, every one of those components needs to go to the right account. Sales income is not the same as the payout amount. Fees are an expense. Refunds reduce income. Shipping labels might be cost of sales or an expense, depending on your client’s chart of accounts. Tax withheld needs proper VAT treatment.
Post the lump sum as income and the P&L is wrong, the VAT return is wrong, and year-end is a mess. Your options have traditionally been:
Option A: Manual spreadsheet
- Download settlement CSV from each platform
- Manually map line items to accounts
- Create journal entries in your accounting software
- Reconcile the control account to the bank payout
- Repeat every settlement period, for every client, for every platform
Option B: Dedicated subscription tool
- Pay £13–229/month per channel
- Connect via API to marketplace + accounting software
- Automated settlement summaries posted as journals
- Separate onboarding, separate login, separate billing
- Only handles merchant data — regular bookkeeping is a different tool
Both work. Neither is ideal. The spreadsheet approach doesn’t scale past a handful of clients. The subscription approach works well but adds cost and complexity to your tool stack — yet another login, yet another monthly bill, yet another piece of software that only solves one part of the bookkeeping puzzle.
The existing solutions: A2X and LinkMyBooks
Credit where it’s due. A2X and LinkMyBooks built their products specifically for this problem, and they do it well. If you’re evaluating merchant bookkeeping tools, you should understand what each offers before considering alternatives.
A2X
Most EstablishedA2X is the market leader in ecommerce settlement reconciliation. It connects directly to marketplace APIs and posts settlement summaries to your accounting software as invoices or journal entries. The mapping is rule-based: you define which accounts each fee type maps to, and A2X applies those rules automatically on every settlement.
Strengths
- Deepest marketplace integrations (Amazon, Shopify, eBay, Etsy, Walmart, BigCommerce, PayPal)
- Supports Xero, QuickBooks, Sage, NetSuite
- Settlement-based summaries keep the ledger clean
- Multi-currency support with proper exchange rate handling
- Trusted by large ecommerce accountancy practices
- Enterprise tier handles high-volume sellers
Limitations
- $29–229/month per channel (adds up fast with multiple platforms)
- Separate subscription from your bookkeeping tools
- Only handles marketplace/merchant data
- Setup requires careful account mapping per client
- No AI categorisation — rule-based mapping only
LinkMyBooks
Most UK-Friendly PricingLinkMyBooks takes a similar approach to A2X but with more accessible pricing and a guided setup wizard that makes initial configuration less daunting. It’s particularly popular with smaller UK practices and individual sellers who find A2X’s enterprise positioning overkill for their needs.
Strengths
- More affordable entry point (£13/mo for one channel)
- Guided setup wizard for account mapping
- Supports TikTok Shop, WooCommerce, Square (A2X doesn’t)
- Good UK-focused documentation and support
- Invoice-level detail available on higher tiers
Limitations
- Xero and QuickBooks Online only (no Sage, no NetSuite)
- Still a separate subscription from regular bookkeeping
- Higher tiers (£49–249/mo) needed for multi-channel
- No AI — same rule-based mapping approach
- Newer product, smaller user base than A2X
The core trade-off with both tools
A2X and LinkMyBooks are excellent at what they do. But they only do one thing: connect marketplace data to your accounting software. Your regular bank statement coding, invoice matching, transfer detection, and VAT classification all need separate tools or manual work. For practices managing clients with both merchant income and normal business expenses, that means two workflows, two sets of tools, and two sets of costs.
A different approach: merchant data inside your bookkeeping workflow
When we built CodeIQ, the focus was on automating the full bookkeeping pipeline: upload a bank statement, AI-categorise every transaction against the client’s chart of accounts, handle VAT, detect transfers, match invoices, and post everything to Xero, QuickBooks, Sage, or Pandle.
Merchant accounts were a natural extension. If you’re already processing a client’s bank statement in CodeIQ, why should their eBay settlement require a completely different tool?
The Merchant Accounts tab does exactly what it sounds like. You upload a merchant settlement CSV — eBay, Amazon, or PayPal — and CodeIQ parses it into individual journal entries. The same AI that categorises bank transactions categorises the merchant line items, using the same chart of accounts, the same learned patterns, and the same review interface. Everything gets posted together.
One workflow, not two
The key difference isn’t technical — it’s operational. There is no separate subscription, no separate onboarding, no separate login. Merchant bookkeeping happens inside the same session as regular bookkeeping. Your bank statement transactions and merchant settlement transactions are reviewed side by side and posted in one batch.
How it works: step by step
Designate a merchant control account
In your client’s chart of accounts (Xero, QuickBooks, Sage, or Pandle), create a bank account representing the merchant platform. This is your control account — “eBay Control”, “Amazon Settlements”, “PayPal Holding”, or whatever naming convention your practice uses. All merchant transactions post here, and the payout to the real bank account clears the balance.
Upload the settlement CSV
Download the settlement report from eBay (Seller Hub → Payments → Reports), Amazon (Seller Central → Payments → Settlement Reports), or PayPal (Activity → Download History). Drop it into CodeIQ’s Merchant Accounts tab. The platform is auto-detected from the file structure — no manual selection needed.
Automatic parsing of all line items
The parser breaks the settlement into individual entries: each sale, each fee type (final value fees, promoted listing fees, shipping labels, international fees), each refund, each adjustment. Platform-specific fee structures are handled automatically — eBay’s managed payments format, Amazon’s settlement report columns, and PayPal’s transaction history format are all recognised.
Payouts are excluded automatically
The payout line (the actual bank transfer from the platform to the client’s bank account) is automatically identified and excluded from processing. That payout is already on the bank statement — it’s the lump sum you’re trying to break down. Posting it again would double-count. CodeIQ handles this so you don’t have to remember to delete it manually.
AI categorisation against your chart of accounts
Each parsed line item is categorised by the same AI pipeline that handles regular bank transactions. It knows that “eBay Final Value Fee” maps to selling expenses, that “Promoted Listing Standard Fee” maps to advertising, that shipping labels map to postage or cost of sales. It uses the client’s actual chart of accounts — not generic categories — and learns from corrections over time.
Review alongside regular transactions
Merchant transactions appear in the same review table as bank statement transactions, distinguished by a merchant platform badge. You review, correct, and approve everything in one pass. No switching between tools. No separate review workflow.
Post everything in one batch
Hit post. Bank statement transactions go to the client’s regular bank account. Merchant transactions go to the control account. The payout on the bank statement (already handled as a transfer) clears the control account. Everything balances. One session, one posting job, one reconciled client.
Head-to-head comparison
| Feature | A2X | LinkMyBooks | CodeIQ |
|---|---|---|---|
| Pricing | $29–229/mo per channel | £13–249/mo | Included in CodeIQ subscription (from £5/mo) |
| Separate subscription? | Yes | Yes | No — built into existing workflow |
| Marketplaces | Amazon, Shopify, eBay, Etsy, Walmart, BigCommerce, PayPal | Amazon, eBay, Etsy, Shopify, Walmart, WooCommerce, TikTok Shop, Square | eBay, Amazon, PayPal |
| Accounting platforms | Xero, QBO, Sage, NetSuite | Xero, QBO | Xero, QBO, Sage, Pandle |
| Data connection | Direct API | Direct API | CSV upload |
| Posting method | Settlement summaries | Settlement summaries | Individual journal entries |
| AI categorisation | No — rule-based mapping | No — rule-based mapping | Yes — learns from CoA + corrections |
| Regular bookkeeping? | No — merchant only | No — merchant only | Yes — bank statements + merchants in one flow |
| VAT handling | Basic tax mapping | Basic tax mapping | Full AI VAT classification |
| Multi-currency | Yes (automatic) | Yes | Limited (uses settlement currency) |
| Inventory/COGS tracking | Yes (higher tiers) | Yes (higher tiers) | No |
| Best for | High-volume multi-channel sellers, enterprise ecommerce practices | UK sellers wanting affordable marketplace automation | Practices wanting one tool for all bookkeeping inc. merchants |
Prices as of March 2026. Check each provider’s website for current pricing. A2X prices in USD; LinkMyBooks and CodeIQ in GBP.
Who this is for
Accountants managing eBay or Amazon sellers alongside regular bookkeeping. If your client sells on eBay and also has normal business expenses, rent, payroll, and supplier invoices, CodeIQ lets you handle everything in one session instead of switching between tools.
Practice owners who want to consolidate their tool stack. Every additional subscription is a cost, a login, an onboarding process, and a support relationship. If you can avoid adding A2X or LinkMyBooks on top of your existing bookkeeping automation, that’s one less moving part.
Sellers who already use Xero, QuickBooks, or Sage for regular bookkeeping. If you’re already having your bank statement processed through CodeIQ, adding the merchant settlement CSV is a two-minute addition, not a separate workflow.
Anyone doing this manually in spreadsheets today. If you’re currently downloading eBay settlement CSVs, mapping line items by hand, and manually creating journals — even the simplest automation is a significant time saving.
What it doesn’t do (yet)
Honesty matters more than a sales pitch. Here’s where CodeIQ’s merchant handling is genuinely limited compared to A2X and LinkMyBooks:
Current limitations
- No Shopify, Etsy, or Walmart support yet. Only eBay, Amazon, and PayPal CSVs are currently parsed. If your clients sell primarily on Shopify or Etsy, A2X or LinkMyBooks are the better choice today.
- No direct API pull. You need to download the settlement CSV from the marketplace and upload it. A2X and LinkMyBooks pull data automatically via API. For high-frequency settlements, the manual download adds friction.
- No inventory or COGS tracking. CodeIQ categorises settlement line items, but it doesn’t track inventory levels, cost of goods sold per SKU, or landed costs. If your client needs inventory-aware bookkeeping, A2X’s higher tiers handle this.
- No order-level matching. A2X and LinkMyBooks can match settlements to individual orders. CodeIQ works at the settlement line-item level — it knows there was a sale for £29.99 and a fee of £3.90, but not which specific order generated them.
- Limited multi-currency. CodeIQ processes in the settlement currency. A2X handles automatic exchange rate conversion for multi-currency marketplaces more robustly.
For a high-volume Amazon seller operating across five marketplaces in three currencies with 50,000 orders a month, A2X is the right tool. It was built for exactly that use case, and trying to handle that scale with CSV uploads would be impractical.
For an accountant with 30 clients, five of whom sell on eBay and three of whom take PayPal payments, adding CodeIQ’s merchant parsing to the existing bookkeeping workflow is simpler and cheaper than adding a separate subscription for those eight clients.
Know your use case. Pick the tool that fits.
Try CodeIQ’s Merchant Accounts
Upload a bank statement and a merchant settlement CSV. See both processed, categorised, and ready to post — in one session.
Try CodeIQ FreeFrequently Asked Questions
How do I reconcile eBay managed payments in my accounting software?
eBay deposits lump-sum payouts to your bank account. To reconcile properly, you need to break each payout into its components: gross sales, eBay fees (final value fees, promoted listing fees, international fees), shipping labels, refunds, and any tax withheld. You can do this manually from eBay’s settlement CSV, use a dedicated tool like A2X or LinkMyBooks to post summaries, or use CodeIQ to parse the settlement into individual journal entries against a control account.
What is a merchant control account and why do I need one?
A merchant control account (sometimes called a clearing account) is a bank account in your chart of accounts that represents the money held by a merchant platform like eBay, Amazon, or PayPal before it reaches your actual bank. You post individual sales and fees to this control account, then reconcile the control account balance to zero when the platform pays out to your bank. This gives you an accurate audit trail rather than posting lump sums to income.
Is A2X worth the cost for eBay and Amazon sellers?
For high-volume sellers with multiple channels, yes. A2X’s deep marketplace integrations, automatic data pulling, and inventory tracking justify the $29–229/month for practices with significant ecommerce client bases. For smaller sellers on one or two channels who already use bookkeeping automation, the additional subscription may not be necessary since the same settlement data can be parsed from within the existing workflow.
How does CodeIQ compare to LinkMyBooks for eBay bookkeeping?
LinkMyBooks pulls settlement data via API and posts summaries to Xero or QuickBooks. CodeIQ takes a different approach: you upload the merchant settlement CSV, and it parses every line item into individual journal entries, AI-categorises them against your chart of accounts, and posts them alongside your regular bank transactions. LinkMyBooks supports more platforms (TikTok Shop, WooCommerce, Square). CodeIQ handles merchant data as part of your existing bookkeeping workflow without a separate subscription.
Can I use one tool for both regular bookkeeping and merchant reconciliation?
Yes. CodeIQ handles both regular bank statement coding and merchant settlement parsing in one workflow. You upload your bank statement as normal, then add merchant CSVs from the Merchant Accounts tab. Both are AI-categorised against the same chart of accounts, reviewed in the same interface, and posted to your platform in one batch.
What merchant platforms does CodeIQ support?
CodeIQ currently supports eBay (managed payments settlement CSVs), Amazon (settlement reports), and PayPal (transaction history CSVs). The parser auto-detects which platform the file came from. Shopify, Etsy, and other marketplace CSVs are not yet supported but are on the development roadmap.
Do A2X and LinkMyBooks post individual transactions or summaries?
Both post settlement summaries, not individual transactions. Each settlement period becomes a single summary invoice or journal entry with line items for gross sales, each fee type, refunds, and tax. This keeps your ledger clean but means you cannot drill down to individual order-level transactions within your accounting software. CodeIQ takes the opposite approach, posting individual journal entries for each line item.