What Makes Pin Payments Reconciliation Different?

Pin Payments is an Australian payment gateway primarily used by Australian and New Zealand businesses to accept card payments online. It operates as a pure payment processor — not a marketplace or ecommerce platform — so reconciliation follows a gateway clearing account model similar to Stripe or PayPal, with several Australia-specific differences that matter for bookkeeping.

Key characteristics that affect QBO reconciliation:

• Daily T+2 settlement: Pin Payments transfers funds to your bank account daily on a two-business-day delay. A charge processed on Monday arrives in your bank on Wednesday. Foreign currency charges add two additional business days (T+4). This timing gap means QBO bank deposits will never match transaction dates — they always trail by at least 2 business days.

• GST is included in all transaction fees for Australian businesses. Pin Payments charges 1.75% + $0.30 AUD for domestic cards, 2.9% + $0.30 AUD for international cards (in AUD), and 3.9% + $0.30 for foreign currency transactions. All these fees include GST at 10% for Australian ABN holders. This means every fee entry in QBO requires a GST code (BAS 1B), and the GST portion is claimable on your BAS. New Zealand businesses pay fees exclusive of GST.

• No refund processing fee. Pin Payments does not charge a fee to process a refund. The original transaction fee is not reversed either. The refund amount is simply debited from your Pin Payments balance.

• Dispute admin fee of $25 AUD (or $25 NZD). When a cardholder raises a formal dispute, Pin Payments withholds the disputed transaction amount plus a $25 AUD (or $25 NZD) admin fee from your settlement funds. If you win the dispute, both the transaction amount and the $25 fee are released back. If you lose, both are permanently deducted.

• Multi-currency support with two settlement options. Foreign currency transactions can be settled either in AUD (converted at the time of the transaction with a 1.7% conversion fee on top of the card fee) or held in one of 7 supported foreign currencies (AUD, NZD, USD, EUR, GBP, SGD, CAD) and transferred to your bank in that currency. Each foreign currency balance settles separately to a designated bank account.

• Individual sync only in PayTraQer. PayTraQer syncs Pin Payments in individual (itemized) mode — one Sales Receipt per transaction, one fee entry per charge, one Transfer per daily settlement. There is no consolidated/summary sync option.

• No native QBO connector. There is no Pin Payments app in the QuickBooks App Store. PayTraQer is the primary integration path.

Understanding Pin Payments Transaction Types

PayTraQer maps the following Pin Payments transaction types into QBO:

How PayTraQer Syncs Pin Payments to QBO

PayTraQer connects to Pin Payments via your Secret API Key and downloads all transaction-level data. The individual sync model works as follows:

1. Each Charge creates one Sales Receipt in QBO, deposited to Pin Payments Bank Account (clearing).

2. Each fee creates one Expense entry, debited from Pin Payments Bank Account.

3. Each Refund creates a Refund Receipt, debited from Pin Payments Bank Account.

4. Each daily Transfer/Settlement creates a Bank Transfer from Pin Payments Bank Account → Business Checking Account.

5. The net balance in Pin Payments Bank Account at any point equals: charges received minus fees minus refunds minus transfers — which should approach $0 daily after settlements clear.
   Critical: PayTraQer's official reconciliation guide for Pin Payments states: "While configuring the settings, you need to select the same bank account (Pin Payments Bank Account or created account) for Sales, Products & Services, Tax and Payouts in PayTraQer." Every single mapping must point to the same clearing account or the reconciliation will break.

Step 1 — Prerequisites and QBO Setup

Create the Pin Payments Clearing Account

1. QBO → Accounting → Chart of Accounts → New

2. Account Type: Bank

3. Detail Type: Checking

4. Name: Pin Payments Bank Account

5. Currency: AUD (Australian Dollar) — set this at creation; cannot be changed later

6. Save and Close.

For businesses settling foreign currency balances separately (e.g., USD payments held in USD):

• Create additional Bank accounts: Pin Payments USD Balance, Pin Payments GBP Balance, etc. — each in the corresponding currency

• Enable Multi-Currency in QBO: Settings → Account and Settings → Advanced → Currency → Multicurrency → Save

Create Income and Expense Accounts

GST Note for Australian Businesses: Pin Payments fees are GST-inclusive at 10%. When you map fees to Pin Payments Fees in QBO, apply the GST (BAS 1B) tax code so QBO automatically calculates the claimable input tax credit. For every $1.75 + $0.30 fee, approximately $0.19 is GST you can claim on your BAS. New Zealand businesses set fees as GST-exclusive and apply the NZ GST code separately.

Download Your Source of Truth from Pin Payments Dashboard

Before reconciling each month:

1. Transaction History CSV: Log in to Pin Payments Dashboard → Transactions → Filter by date range → Export CSV. This lists every individual charge with charge token, amount, date, card type, and fee amount. This is your line-by-line verification source.

2. Transfer History CSV: Pin Payments Dashboard → Transfers → Export CSV. This lists every daily settlement to your bank account, with the transfer token, amount, date, and status. The transfer amounts are what you match in QBO's bank feed.
   Tip: The Transfer date in the Pin Payments dashboard is the date Pin Payments initiated the transfer — not the date it arrived in your bank. Your bank receives the funds T+2 business days later. When matching in QBO, look for the corresponding bank deposit 2 business days after the transfer date shown in Pin Payments.

Step 2 — Connecting Pin Payments to PayTraQer

Get Your Pin \API Key

1. Log in to your Pin Payments Dashboard

2. Go to Your Account → API Keys

3. Copy your Secret API Key (the live key, not the test/sandbox key)
   Never use the Test API Key for a live QBO company — it syncs test transactions that do not correspond to real income.

Connect in PayTraQer

1. Log in to PayTraQer → Connectors → + Add New → Payment Platforms → Pin Payments

2. Enter your Secret API Key

3. Select your QBO company

4. Click Authorise → PayTraQer confirms connection

5. PayTraQer automatically downloads the past 60 days of Pin Payments transactions on first connection

Step 3 — Configuring PayTraQer Settings for Pin Payments

In PayTraQer → Settings → Pin Payments. Every single mapping in every tab must point to Pin Payments Bank Account.

Sales Settings

• Bank Account to Deposit: Pin Payments Bank Account

• Income Account: Pin Payments Sales

• Payment Method: Pin Payments

• Customer: Common Customer (Pin Payments Customer) — recommended; prevents customer list bloat from one-off ecommerce buyers

Products & Services Settings

• Common Product/Service: ON

• Item Name: Pin Payments Sale

• Income Account: Pin Payments Sales

• Bank Account: Pin Payments Bank Account

Tax Settings

For Australian businesses (GST-registered):

• Apply GST tax code to sales (if your sales are taxable)

• Map fee tax to GST (1B) — this is the input tax credit code on your BAS for the GST included in Pin Payments fees

For New Zealand businesses (GST-registered):

• Apply NZ GST codes as appropriate — Pin Payments NZ fees are GST-exclusive, so the GST component is added on top

Fees Settings

All fee types must use Pin Payments Bank Account as the Bank Account. This is non-negotiable. If any fee points elsewhere, the clearing account will not balance.

Payout Settings

• Enable "Process the Payout": Toggle ON

• Transfer Account: Your real Business Checking Account (AUD)

• For foreign currency settlements: create separate Transfer Accounts per currency (e.g., USD Checking for USD settlements)

When ON, PayTraQer creates a Bank Transfer from Pin Payments Bank Account → Business Checking Account for each daily settlement. This is what you match in QBO's bank feed.

Step 4 — Syncing Transactions and Verifying in QBO

Running a Sync

1. PayTraQer → Connectors → Pin Payments → Transactions Dashboard

2. Set the date range for your target period

3. Click Download Transactions

4. In the Not Synced tab, review a sample of transactions:

   • Charges show Pin Payments Bank Account as the deposit account

   • Fee entries show correct expense account and Pin Payments Bank Account as bank

   • Transfers show Bank Transfer to Business Checking Account

5. Click Sync to QuickBooks

6. Monitor the Synced and Error tabs — resolve any errors before proceeding to reconciliation

Verify in QBO

QBO → Accounting → Chart of Accounts → Pin Payments Bank Account → View Register

Confirm:

• Individual Sales Receipts per charge

• Fee expense entries per transaction

• Daily Bank Transfers to Checking (one per Pin Payments daily settlement)

• Running balance approaches $0 daily after each transfer clears

Step 5 — Matching the Bank Feed in QBO

When a Pin Payments settlement arrives in your bank (T+2 business days after the transfer date):

1. QBO → Banking → For Review (your Business Checking Account)

2. Find the Pin Payments deposit — it typically appears as "PIN PAYMENTS" or "PINPAYMENTS" in the payee column

3. QBO will suggest a green Match to the PayTraQer Bank Transfer

4. Click Match
   Never click "Add." Clicking Add records the settlement as new income — duplicating all the Sales Receipts PayTraQer already posted to Pin Payments Bank Account.

If the Deposit Doesn't Match

• Date mismatch: The transfer arrived T+2 but PayTraQer dated it at the initiation date. Expand the date window in QBO's Match screen.

• Amount mismatch: A same-day refund or dispute hold altered the settlement net. Cross-reference the Pin Payments Transfer History CSV for the exact transfer amount and its components.

• Multiple same-day charges, one settlement: Pin Payments consolidates all same-day AUD charges into a single daily transfer. The PayTraQer Bank Transfer should equal the sum of all that day's charges minus fees. If the amounts differ, check the Transfer History CSV for the exact settlement breakdown.

Bank Rule for Ongoing Efficiency

1. QBO Banking → Rules → New Rule

2. Condition: Bank text contains "PIN PAYMENTS"

3. Action: Transfer from Pin Payments Bank Account

Step 6 — Reconciling the Accounts in QBO

Reconcile the Pin Payments Bank Account

1. QBO → Accounting → Reconcile

2. Account: Pin Payments Bank Account

3. Ending Balance: Enter the closing balance from your Pin Payments Dashboard on the last day of the month. For most merchants, this is $0.00 or a very small amount representing charges from the last 1–2 business days of the month that have not yet been settled (in-transit T+2 funds).

4. Ending Date: Last day of the month

5. Click Start Reconciling

6. Check off:

   • All Sales Receipts (individual charges)

   • All fee expense entries

   • All refund entries

   • All Bank Transfers to Checking (daily settlements)

   • Any dispute admin fee entries

7. Difference must read $0.00

8. Click Finish Now → save the reconciliation PDF

Understanding the In-Transit Balance

Unlike Amazon Pay (which carries a reserve), Pin Payments settles daily. The only reason Pin Payments Bank Account will show a non-zero ending balance is in-transit funds — charges processed in the last 1–2 business days of the month that Pin Payments has not yet settled. This is a timing difference, not a reserve.

Example: If the month ends on Friday 31 March, charges from Wednesday 29 March (T+2 = Friday settlement) will clear, but Thursday 30 March charges (T+2 = Monday 1 April) and Friday 31 March charges (T+2 = Tuesday 2 April) will not yet appear in your bank. Those amounts sit in Pin Payments Bank Account as the ending balance. Enter this in-transit amount as the Ending Balance in QBO reconciliation.

Reconcile the Main Bank Account

After Pin Payments Bank Account reconciliation is complete, proceed with your standard bank reconciliation. All matched Pin Payments settlements will already be cleared.

GST on Fees: BAS Reconciliation for Australian Businesses

This section applies only to Australian GST-registered businesses. Skip for New Zealand or international merchants.

Pin Payments states clearly: "For Australian based businesses, Goods and services Tax (GST) is included on transaction fees at the current rate of 10%."

This means every Pin Payments processing fee contains a GST component you can claim as an Input Tax Credit (ITC) on your quarterly or monthly BAS (1B GST on purchases).

How to verify the GST claim in QBO:

1. Run QBO → Reports → GST Summary Report for the period

2. The GST on Pin Payments Fees should appear under 1B — GST on Purchases (claimable credits)

3. Cross-check: total fees in Pin Payments Transaction CSV × (10/110) = GST component

4. This GST amount should match the ITC amount showing in the BAS report for Pin Payments fees

Example:

• Monthly processing fees: $580.00 AUD (GST-inclusive)

• GST component: $580 × (10/110) = $52.73 AUD claimable on BAS

If the GST code was not applied in PayTraQer Fee Settings, correct it:

• In PayTraQer → Settings → Pin Payments → Fees Settings → add GST (1B) tax code to all fee types

• Roll back the affected period's sync → re-sync with correct tax code

Common Pin Payments Scenarios and Fixes

Final Month-End Checklist for Pin Payments + QBO Reconciliation

• Pin Payments Transaction History CSV downloaded for the period

• Pin Payments Transfer History CSV downloaded — all settlement amounts and dates noted

• In-transit balance calculated (charges from last 1–2 business days not yet settled) — noted as QBO Ending Balance

• All transactions confirmed "Synced" in PayTraQer — Error tab is empty

• All fee mappings confirmed pointing to Pin Payments Bank Account

• GST (1B) tax code applied to all fee entries in PayTraQer (Australian businesses)

• Dispute admin fees ($25 AUD) mapped to Pin Payments Dispute Fees expense

• Any dispute win reversals verified in QBO — $25 fee and disputed amount correctly reversed

• Each Pin Payments bank deposit Matched (not Added) in QBO Banking For Review

• Bank rule for "PIN PAYMENTS" confirmed as Transfer from Pin Payments Bank Account

• Pin Payments Bank Account clearing reconciled — Ending Balance = in-transit amount — Difference $0.00

• BAS GST report reviewed — Pin Payments fee GST appearing correctly under 1B (Australian businesses)

• P&L reviewed: Pin Payments Sales shows gross captures; Pin Payments Fees shows all processing costs; dispute fees tracked separately

• Reconciliation PDF saved to client folder