đ Note: This is the single most common question new Method Pay customers ask. If your deposit doesn't match your invoice total, nothing has gone wrong. The difference is the fee and it's itemized for you in the transaction record.
Method Pay fees are netted out of each deposit as it's paid. There is no monthly invoice and no lump-sum debit at the end of the billing period.
That means the amount that lands in your bank account is the payment amount minus fees. It is not the full amount your customer paid.
When the deduction actually happens
Fees are not taken at the moment your customer clicks Pay. They come out when the payment is released for deposit.
Payment type | Deposit timing | Daily cutoff |
Card | T+1 (next business day) | 11:00 PM ET |
ACH | T+4 (four business days) | 9:00 PM ET |
Validated ACH | Configurable | 9:00 PM ET |
Refunds | T+1 | â |
*Payments submitted after the cutoff use the next day as T.
Example: A card payment taken Monday afternoon deposits Tuesday, with the fee already deducted from that Tuesday deposit. An ACH payment taken Monday deposits Friday, with its fee deducted from Friday's deposit.
What makes up a deposit
You receive one deposit per US banking day by default, covering every payment ready for release that day. Each deposit is the sum of the payments, minus the fees on those payments and minus the daily deposit fee.
Example: a day with three card payments
Line | Amount |
Three card payments totalling | $1,200.00 |
Processing fees (example rate 2.99% + $0.30 per transaction) | â$36.78 |
Daily deposit fee | â$0.25 |
Net deposited to your bank | $1,162.97 |
Each individual payment record shows its own Net to merchant figure, so you can trace any single transaction back to what you actually received.
đ Note: Rates shown here are illustrative. For the rates that apply to your account, see the Method Pay Payment Processing Agreement or contact your Platform Success Manager.
The daily deposit fee
A flat daily deposit fee applies on any day a deposit is issued. One deposit per day means one fee per day. It does not scale with the number of transactions or the value of the deposit.
At normal volumes this is spread across many payments and barely visible. On a light day it's more noticeable.
Why a test transaction looks wrong
This trips up almost everyone during setup. If you run a single small test payment â say $1.00 â you'll see two fees hit the same deposit:
Line | Amount |
Test payment | $1.00 |
Processing fee on the transaction | â$0.33 |
Daily deposit fee | â$0.25 |
Net deposited | $0.42 |
Losing more than half of a $1.00 test looks alarming, but it's the correct behaviour. You're seeing the per-transaction fee and the once-a-day deposit fee land on the same tiny deposit. At real invoice values the deposit fee is immaterial.
Fees that appear as adjustments
Some charges aren't tied to a single incoming payment. These are applied as adjustments against your deposit rather than as a separate bill.
Fee | When it applies |
ACH return fee | An ACH payment is returned by the customer's bank |
Chargeback / dispute fee | A chargeback is created, regardless of the outcome |
Refund processing fee | You issue a refund on a settled transaction |
3D Secure attempt fee | Each 3DS attempt, if 3DS is enabled |
Card Account Updater fee | Each stored card replaced or disabled by CAU, if enabled |
If a return or chargeback lands on a day when you're also receiving payments, it's netted against that deposit. For detail on returns specifically, see How ACH Returns are handled & fees. For chargebacks and refunds, see Handling Disputes in Method Pay.
Finding your deposits and fees
In Method: go to Profile â Integrations â Payment Gateways â View Method Pay transactions.
The Deposits tab under Reports shows the real-time status of each deposit. The Payments tab shows each transaction with its fee and net amount.
On your bank statement: deposits use a standard descriptor format so you can match them back.
đ Note: Some entries show a RF prefix. This refers to the payment processing infrastructure behind Method Pay and is expected â it is not an error or a third-party charge.
Recording fees in QuickBooks
Because fees are deducted before the deposit arrives, the deposit in your bank feed won't match the invoice you issued. To keep the books clean, record the full payment against the invoice and create an offsetting bill to Method Pay as a vendor for the fee amount.
For a walkthrough, see Method Pay - Record Deposits in QuickBooks Online.
đ Note: If you're coming from a processor that deposited the gross amount and posted fees as a separate transaction, this is the main difference you'll notice. The end result in your books is the same, the entry is just made once rather than automatically.