A plan manager's payment run lands in your client's bank account as a single deposit. Behind that one line are dozens of invoices across many participants, and the explanation arrives separately, as a remittance advice in PDF or CSV. The references on it are claim numbers and participant codes, not your Xero invoice numbers. Some invoices are paid in full. Some are part paid.
This guide is for the people who reconcile those deposits: bookkeepers and accountants with NDIS providers on their client list, and the practice managers and finance staff inside provider businesses, from allied health and therapy through to support coordination and SIL. It covers what Xero can and cannot do with a plan manager remittance, what a properly reconciled payment run looks like, and how EntryRocket automates the work.
Why this is worse than ordinary reconciliation
Most bank reconciliation is one statement line against one invoice. A plan manager run breaks that in several ways at once. Claims get part paid, so the payment against an invoice is less than its total. An invoice can be settled across two payment runs, with the balance arriving weeks after the first instalment. Remittances carry negative adjustment or rejection lines that pull the deposit total away from the sum of the invoices. And the reference the plan manager quotes is usually theirs, not yours, so before you can apply anything you first have to work out which Xero invoice each line belongs to.
Then there is the format problem. There is no such thing as "the NDIS remittance format". The NDIS Quality and Safeguards Commission counted more than 1,100 plan managers in its Own Motion Inquiry into plan management (June 2023 quarter), and each one designs its own remittance layout. A provider with five payers deals with five different documents; a bookkeeper with five NDIS clients deals with far more. Whatever process you build for one plan manager does not transfer to the next.
What Xero gives you, and where it stops
To be fair to Xero first: Find and Match works fine for small runs. Open the bank reconciliation screen, click Find and Match, tick invoices until they add up to the deposit, adjust for any part payment, and reconcile. For a deposit covering a handful of invoices this is a perfectly good workflow.
It stops being good when the run gets long. The obvious upgrade is to build a batch deposit: go to the Awaiting Payment list, select the invoices the remittance covers, and choose Deposit. That works up to a hard limit. Select more than 50 invoices and Xero refuses with this exact message:
Too many invoices to pay. You cannot create a deposit for more than 50 invoices.
Nothing is created. We verified this against a live Xero organisation in July 2026: 60 selected invoices, one click of Deposit, and a dead end. That 50 is the limit on building a deposit by hand, not the end of the story.
Xero knows about the problem. The product idea "Batch deposit more than 50 transactions" has been open on Xero's forum since April 2022 and has 90 votes; Xero staff responded on 9 July 2025 that it is "not planned in the short term". The other obvious escape route, importing the payments from a file, is closed too. On a separate product idea asking for exactly that, Kelly Munro, Xero Community Manager, wrote on 26 June 2026: "we don't currently have plans to support importing received payments." That idea has 32 votes and sits at Gaining Support. So for large payment runs, Xero's built-in answer today is Find and Match, one invoice at a time.
What the reconciled result should look like in Xero
Done properly, one payment run becomes one batch deposit in Xero, and its total equals the bank statement line to the cent. Every invoice the remittance settled in full is marked paid. Every part paid invoice stays in Awaiting Payment showing the correct outstanding balance, so nothing quietly disappears from your receivables.
When the bank line comes through the feed, Xero matches it against the batch deposit and the reconciliation is one click. No suspense account, no receive money entry parked against a clearing code, no spreadsheet on the side tracking which invoices the deposit was supposed to cover. For the mechanics of the Xero object itself, see creating a Xero batch deposit from a file.
How EntryRocket does it
You email the remittance advice to a dedicated EntryRocket address, exactly as the plan manager sent it. A reader built for that plan manager's layout knows where your invoice numbers sit among the claim references, works out how much was paid against each invoice, and creates the batch deposit in your Xero organisation. Part payments are recorded at the amount actually paid, so the invoice keeps its outstanding balance.
Because the batch deposit is created through the Xero API rather than the Xero screen, the 50-invoice limit does not apply. In our July 2026 test against a live Xero organisation, a 60-invoice remittance produced a single batch deposit of $13,216.20 with all 60 payment lines and no errors.
The ceiling is 200 invoices, and that one is Xero's. At 250 invoices Xero rejects the entire batch with "Batch payments cannot be created for more than 200 payments". (Xero says payments because the same feature pays bills in bulk.) Nothing partial is written, no credits are charged, and the import report tells you what happened. But nothing is created either: a remittance over 200 invoices needs splitting by hand today, and we do not currently work around that limit. The working range for a single batch deposit through EntryRocket is 51 to 200 invoices, four times what the Xero screen allows.
For bookkeepers and accountants with several NDIS clients
Plan management is not a corner case in your client base. The NDIS Quality and Safeguards Commission reported that payments managed by a plan manager rose from 38 per cent to 53 per cent of total NDIS payments in the two years to the June 2023 quarter. If you look after NDIS providers, most of the money in their bank feeds now arrives as plan manager deposits, and every one of them lands on your desk per client, per payment run, fortnight after fortnight.
This is where automating the match pays for itself fastest, because the work multiplies across the client list rather than growing within one file. Each of your clients' Xero organisations gets its own dedicated EntryRocket address, so forwarding a remittance takes seconds from wherever it arrives, and there is no risk of one client's payment run landing in another's books. A plan manager sends the same remittance layout to every provider it pays, so the format knowledge from one client carries directly to the next. Plans are sized by the number of connected Xero organisations.
Plan managers we already read
We already read remittances from Plan Partners, Leap In, MyIntegra, NIB Thrive, Bright Plan Management and others, so most of the common formats are not new to us. Each reader is set up for a specific provider's Xero organisation, so this is not a list of integrations you switch on. It does mean that when your payer is one of these, the file holds no surprises for us.
Either way, the starting point is the same: send us a sample remittance, exactly as it arrived, and we will tell you what the reconciled result would look like in your Xero.
Claiming is not reconciling
Two different jobs get mixed up in NDIS bookkeeping conversations. Claiming is getting paid: submitting payment requests through myplace and PRODA for agency-managed participants, or invoicing the plan manager for plan-managed ones. Practice management software handles claiming well, including uploading bulk payment requests and matching the results file.
Reconciling is accounting for the money after it lands: turning the deposit in the bank into paid invoices in Xero. That is the gap this page is about, and it exists whether claiming went smoothly or not. For agency-managed payments, we read the NDIA myplace payment-request export too, and turn it into a batch deposit the same way as a plan manager remittance.
What to do when a remittance does not balance
Reconcile to the remittance, not to what you invoiced. The remittance is the payer's statement of what was actually paid, and when it disagrees with your expectations the difference usually has one of a few causes: a claim was rejected or adjusted (a missing or negative line), an invoice was part paid, or the rest of an invoice is coming in a later run.
Resist the urge to force the numbers. A part paid invoice should stay in Awaiting Payment for the balance, because that balance often arrives in the next run after the claim is resubmitted. Only when you know a shortfall is permanent should it be dealt with deliberately, as a credit note or write-off, rather than buried in a rounding adjustment.
EntryRocket applies the same discipline automatically. The batch deposit reflects what the remittance says was paid, no more: part payments go on at their actual amounts, so every outstanding balance stays visible in Xero. If Xero refuses the batch, nothing partial is written.