Reconciliation
How to reconcile Paystack, Flutterwave and Moniepoint settlements with your bank
Your dashboard shows the day's sales, and the next day one smaller credit lands in the bank, covering twenty or two hundred payments with a narration that tells you almost nothing. Add Flutterwave and a few Moniepoint terminals, and the cash book stops agreeing with the bank.
To reconcile them: group each processor's transactions into payouts, recompute the fee and VAT on every one, and agree each payout's net to a bank credit. Whatever is left is a refund, a chargeback, a late payout or an overcharge, and each needs an owner.
What each processor publishes
These are the figures on each company's own website, checked November 2026. Pricing changes and some businesses agree their own rates, so check the live pages and your merchant agreement.
| Paystack | Flutterwave (Nigeria) | Moniepoint POS | |
|---|---|---|---|
| Local payments | 1.5% + ₦100 | 2% (1.4% transaction fee plus 0.6% platform fee) | Not published on the page we checked |
| Small payments | ₦100 waived below ₦2,500 | No waiver shown | Not published |
| Cap | ₦2,000 per transaction | No cap shown | Not published |
| VAT on fees | Not stated on the pricing page | 7.5% | Not published |
| Settlement | T+1, the next working day | Next-day local payouts | "Instant settlement" advertised |
| Source | Paystack pricing | Flutterwave pricing | Moniepoint POS terminals |
The four numbers on every settlement
- Gross: what the customer paid. This is your sale.
- Fee: what the processor charged, on its published or agreed rate.
- VAT on the fee: where the processor adds it, as Flutterwave states it does.
- Net: gross less fee less VAT. This is what should reach the bank.
Book it through a payment gateway clearing account. When the sale happens, debit clearing with the gross and credit sales. When the payout arrives, debit the bank with the net, debit fees and VAT on fees, and credit clearing with the gross. Anything left in clearing is unexplained. A clearing account that returns to zero is the proof that sales, fees and payouts agree.
Batching: many sales, one payout
Paystack might settle all of Monday's card sales as one credit on Tuesday, and Friday's on Monday, later after a public holiday. So you match many lines to one:
- Download the settlement or payout report.
- Group the transactions by payout reference or settlement date.
- Add up gross, fees and VAT for each group.
- Agree each group's net to a bank credit, by amount and date.
A worked example, with fees recomputed
Example figures: a Lagos online store, Monday 12 October.
Paystack. Four card payments, settled as one payout on Tuesday.
| Sale | Gross (₦) | 1.5% (₦) | + ₦100? | Fee (₦) | Net (₦) |
|---|---|---|---|---|---|
| 1 | 2,000 | 30 | Waived | 30 | 1,970 |
| 2 | 10,000 | 150 | Yes | 250 | 9,750 |
| 3 | 50,000 | 750 | Yes | 850 | 49,150 |
| 4 | 200,000 | 3,000 | Yes | 2,000 (capped) | 198,000 |
| Total | 262,000 | 3,130 | 258,870 |
If Tuesday's Paystack credit is ₦258,870, it agrees. If it is ₦257,870, you are ₦1,000 short: look for a refund or chargeback in the report. Note sale 4: without the cap the fee would be ₦3,100. A fee above ₦2,000 on one local payment is an overcharge to query.
Flutterwave. Three payments totalling ₦100,000, settled the next day. At 2% the fee is ₦2,000, and VAT at 7.5% on the fee is ₦150, so the net is ₦97,850. The journal: debit bank ₦97,850, debit processor fees ₦2,000, debit VAT on fees ₦150, credit payment gateway clearing ₦100,000.
Whether VAT on processor fees can be claimed as input VAT depends on your position. Confirm the rules that apply to you with your tax adviser.
Moniepoint POS. With instant settlement advertised, each day's sales should reach the account that day. Agree the day's terminal report to the day's credits, and use the rate in your merchant agreement to check the fee.
Refunds, chargebacks and reversals
- Refunds may be netted off a later payout, so Thursday's payout can be short because of last week's sale.
- Chargebacks are raised by the customer's bank and can move quickly.
- Reversals of failed payments may show as a debit and a matching credit, or not at all.
Treat each as an open item with an owner until it is recovered or written off with approval.
| What you see | What it usually means | What to do |
|---|---|---|
| Payout smaller than expected | Refund, chargeback or wrong fee | Recompute fees from the report |
| No payout today | Weekend, holiday or delay | Check the settlement date, then query |
| Fee above the cap or rate | Overcharge | Raise it with the transaction reference |
| Clearing balance growing | Unmatched sales or unbooked fees | Age it and assign owners |
For terminal-by-terminal work, see how to reconcile POS transactions.
How Brillrec helps
Brillrec is the finance operations platform for Nigerian businesses, with three products: Reconciliation, Internal Control Automation and Financial Close Management.
- Processor connections on Essential and above. In Reconciliation, Paystack, Flutterwave and Monnify (Moniepoint's gateway) bring settlements and their payments, using your own read-only keys. Squad connects too. Bank statements come by upload on every plan, and by Mono bank feed or email on Essential and above.
- Every settlement proved. Payments are grouped into their settlement, and Brillrec checks that gross, less fees, VAT and deductions, equals what reached the bank. Payouts are matched by settlement reference, then net amount, then as grouped or split payouts.
- Fees recomputed against the published prices of Paystack, Flutterwave, Monnify and Squad, and for Moniepoint or any other processor once you enter your agreed rate. Overcharges are listed by month.
- Moniepoint POS. Moniepoint business statements and POS exports are recognised by name. Declined payments are left out and counted. For bank POS, Brillrec checks that each day's net reached the bank.
- The whole statement sorted. A settlement reconciliation takes the entire bank statement and sorts every line into this processor's settlements, another processor's lines, or lines set aside, so the statement still has to add up.
- Daily reconciliation on Essential and above, so a short payout is found the next morning.
- Clearing accounts on Professional and above. Payment gateway clearing, POS clearing and wallet float: every item matched, or aged and owned.
- Late payouts and recoveries: a payout calendar (Professional and above) that marks a Paystack, Flutterwave or Monnify payout late if it isn't in by 10am the next working day, with Nigerian holidays counted; overcharge recovery tracking (Raised, Recovered, Closed); and a disputes register for chargebacks, refunds and reversals (Essential and above).
Our POS and payments page has more. If you run wallets or NIP transfers, read settlement reconciliation for fintechs.
Frequently asked questions
How much does Paystack charge per transaction in Nigeria?
Paystack's pricing page lists 1.5% + ₦100 for local transactions, with the ₦100 waived below ₦2,500 and fees capped at ₦2,000 (checked November 2026).
When does Paystack settle to my bank account?
Paystack lists T+1, the next working day. Friday's sales usually arrive on Monday, later after a public holiday.
Does Flutterwave charge VAT on its fees?
Yes. Its Nigeria pricing page says fees attract 7.5% VAT. The local payment fee is 2%, with no cap shown.
Start your free 14-day trial, no card needed, or book a 20-minute demo.