How to Reconcile Jane Payments Payouts in QuickBooks (or Xero)

If you run a clinic on Jane and take card payments through Jane Payments, you have probably noticed the same thing every bookkeeper notices. The money that lands in your bank never matches what Jane says you sold that day. You billed $2,140 on Tuesday, and three days later $1,663.28 shows up in the account. The numbers are close enough to feel related and far enough apart to be maddening.

Nothing is wrong. This is just how Jane Payments works, and once you understand the two reasons the deposit is off, the fix is a standard piece of bookkeeping that takes a few minutes a month. This article walks through why it happens and exactly how to record it, whether your books are in QuickBooks Online or Xero. The method is the same in both.

Why the bank deposit is never a day's sales

There are two things happening at once, and they stack.

One: the payout is batched, not daily. Jane Payments runs on Stripe underneath, and payouts land on a rolling two-business-day schedule. A card charge you take Monday does not deposit Monday. It gets bundled with other charges from the same processing day and lands in your bank roughly two business days later. Weekend charges batch together and deposit midweek. A stat holiday pushes everything a day. So the deposit that hits Wednesday is not Wednesday's sales. It is a batch of charges from a couple of days back, and the calendar day it represents almost never lines up with the day it arrives.

Two: the deposit is net of fees. Jane Payments takes a processing fee of roughly 2.75% off the top before the money moves. That fee is never a separate line on your bank statement. You do not see a $2,140 deposit and a matching $58.85 fee withdrawal. You see one deposit of $2,081.15 (or whatever the batch nets to), and the fee has already been quietly removed. Your bank feed has no idea the gross amount was ever bigger.

Put those together and you get a deposit that is (a) made up of charges from a day or two ago, (b) bundled with other days, and (c) already shrunk by fees you never see leave. Of course it does not tie to a single day's invoices. It was never going to.

The double-count trap that inflates your revenue

Here is where clinics on Jane quietly get their books wrong, and it is worth slowing down on because it is the expensive one.

The instinct, when a $2,081.15 deposit lands, is to record it as income. Money came in, book it as revenue. But you have almost certainly already recorded that revenue somewhere else, on the invoice, when the sale happened. If you are importing your Jane sales or booking revenue off the Sales Report, the sale is already on your books as income. Then the deposit lands and gets coded to income a second time.

Now the same money is counted twice. Your revenue is overstated by the size of your card deposits, which for a busy clinic is most of your revenue. You will pay tax on income you did not earn, your margins will look better than they are, and if you pay practitioners a percentage of collected revenue, you may be over-calculating comp on inflated numbers.

The deposit is not income. It is the cash arriving for income you already recorded. Those are two different events, and the bank deposit should never touch a revenue account. That is the whole game.

The fix: a Jane Payments clearing account

The clean way to handle this is a clearing account. It is a single account on your balance sheet that acts as a holding pen between "the sale happened" and "the cash arrived." Every clinic on Jane taking card payments should have one. Here is how it works in plain terms.

Set up the account. In your chart of accounts, create a new account called something like Jane Payments Clearing or Undeposited Card Funds. In QuickBooks Online, make it a Bank or Other Current Asset account. In Xero, make it a Current Asset, and tick "Enable payments to this account" so you can reconcile against it. This account should sit near zero most of the time and should net to zero once every payout has landed.

When the sale happens, the card money goes INTO clearing. As you record daily sales, the portion collected on card is debited to the clearing account, not to the bank. The revenue is credited to income as usual (and any GST or HST to the tax payable account). So the sale posts income and parks the cash in clearing, waiting for the bank.

When the payout lands, it comes OUT of clearing. When the net deposit hits your bank, you record it as a transfer out of clearing into the bank, plus the fee. The deposit clears the gross amount out of the holding account, and the fee is booked to an expense account. Nothing hits revenue. The income was already recorded at the sale.

Done this way, the clearing account balance at any moment equals the card money Jane has captured but the bank has not yet paid out. At month-end it should equal the gross value of the payout batches still in transit, to the penny. When those deposits land in the new month, the account nets back to zero.

The journal entries, concretely

Let's use round numbers so you can see the shape. Say on a given day you collected $1,000 in card sales through Jane Payments. That is $1,000 gross. Jane's fee at roughly 2.75% is $27.50, so the eventual bank deposit for that batch will be $972.50.

Step 1. Record the sale (the day it happens). This is your normal revenue entry. The card portion goes to clearing instead of the bank.

Debit   Jane Payments Clearing        1,000.00
Credit  Service Revenue               1,000.00

(If part of that sale carries GST or HST, split the credit between revenue and the tax payable account. Keep the debit to clearing at the full amount the client's card was charged, tax included, because that is what Jane captures and what the payout will be built from.)

Step 2. Record the payout when it lands in the bank (two business days later). The bank receives $972.50 net. The fee comes out of clearing at the same time.

Debit   Bank (chequing)                 972.50
Debit   Merchant Processing Fees         27.50
Credit  Jane Payments Clearing        1,000.00

After both entries, the clearing account is back to zero for that batch. The $1,000 that went in has come out: $972.50 to the bank, $27.50 to fees. Revenue was recorded once, at the sale. The bank shows the real deposit. The fee is captured as a deductible expense instead of vanishing. Everything ties.

In practice you are not doing this one sale at a time. You batch it. Most clinics post the card sales into clearing for a whole day or a whole month in one entry off the Jane reports, and then clear each payout batch out as it lands. The mechanic is identical, just aggregated.

How to handle the fees

The fee is real money and it is a deductible business expense, so give it a home. Create an expense account called Merchant Processing Fees or Jane Payments Fees and post every fee there, the way Step 2 does above. Over a year this adds up to a meaningful number, often a few thousand dollars for a busy clinic, and you want it on the books as an expense, not buried inside a netted-down revenue figure where it silently shrinks your income and your fee deduction both.

You can pull the exact fees two ways. The Daily Transactions Report export, formatted for QuickBooks and Xero, lists processing fees as a negative line item per day. Or the Jane Payments Transactions Report gives you fee-per-charge detail if you want to reconcile down to the transaction. For most closes, the daily fee total is enough.

Why you cannot rely on the Daily Transactions Report alone

This is the trap that catches even careful bookkeepers, so it is worth stating flatly. Jane Payments card revenue does not show up in the Daily Transactions Report. That report captures cash and Interac and other methods, but the card charges run through Jane Payments are not in it. If you build your revenue off the Daily Transactions Report and nothing else, you will miss all of your card income, which for most clinics is the majority of what they take in.

To get the card side, you have to pull the Jane Payments reports separately:

• The Jane Payments Transactions Report gives you every card charge, the gross amount, the fee per charge, and the net paid to the clinic. This is your card revenue and your fee detail.
• The Jane Payments Payouts Report gives you each bank deposit: the date it was created, the date it deposits, and the payout amount after fees, which is what actually lands in your account. This is what you reconcile the bank against.

So a real Jane close is not one report. It is the Sales Report or Daily Transactions for the non-card side, plus the two Jane Payments reports for the card side, reconciled together. Skip the Jane Payments reports and your books will be short by your entire card volume.

Reconciling the bank

Once the clearing method is in place, the monthly bank reconciliation gets simple. Each Jane Payments deposit on your bank statement matches a payout in the Jane Payments Payouts Report, dollar for dollar, because the payout amount is already stated net of fees. You tick each one off against the clearing account. Anything left sitting in clearing at month-end is money Jane captured that has not deposited yet, which you can prove against the payout batches dated in the last day or two of the month that settle early in the next one. That in-transit balance is not an error. It is the timing gap, and it should clear itself when the deposits land.

If your clearing account nets to zero across the boundary and the leftover balance matches the in-transit batches, your card reconciliation is done and it is right.

One more wrinkle: refunds

If you refund a client's card, Jane nets that refund against your next payout rather than sending it as its own line. So a payout can come in smaller than expected, or in a slow week even go negative and pull from your bank account. The clearing method handles this cleanly, because the refund reduces both the revenue side and the clearing balance, and the smaller (or negative) payout still clears the account correctly. Just know that a payout that looks light may have a refund baked into it, and the Jane reports will show you which charge it relates to.

Getting this right once, in a clearing account with fees booked properly and the Jane Payments reports pulled alongside the sales, is the difference between books that reconcile on the first pass every month and books someone has to re-derive every quarter to explain the gap between Jane and the bank.