The quick answer
Turn on Consolidated Payments under Setup > Company > Enable Features, on the Accounting subtab. Then go to Transactions > Customers > Accept Customer Payments and choose the parent customer in Customer. The Apply subtab lists open invoices for the parent and every subcustomer under it, with the subcustomer named in Project/Sub. Type the check total in Payment Amount, check Apply on the invoices the check covers, confirm Unapplied is 0.00, and save. The covered invoices are paid in full and each store's balance drops. The parent's own Balance drops only by what went to its own invoices, while its Consolidated balance drops by the whole payment.
The screenshots show sample data. Person and operating-company names are fictional. Use your own records and values when following the steps.
Before you start
You need a role that can edit company features, or someone who can check them for you, plus permission to view customers and accept customer payments. Consolidated Payments is an account-wide feature. Talk to whoever owns your A/R process before you turn it on, since it changes which invoices show up when anyone accepts a payment from a parent customer. In OneWorld, Consolidated Payments and Multi-Subsidiary Customer can't both be enabled, so if you use Multi-Subsidiary Customer this approach isn't available.
The subcustomers have to exist already. A subcustomer is a normal customer record whose Parent Company field names another customer. It has its own invoices, terms, and balance. To create one, open the parent, go to the Relationships subtab, and click New Subcustomer under Subcustomers. That opens a new customer record with Parent Company already filled in. You can also go to Lists > Relationships > Customers > New and pick the parent in Parent Company yourself. The recording starts with the stores already set up, so it doesn't show this part.
In this example, Alder Valley Foods is a grocery chain, and two of its stores, Millbrook Store and Harbor Street Store, are its subcustomers. There are four open invoices: INV-6120 for 1,960.00 billed to Alder Valley Foods, INV-6134 for 2,420.00 billed to Millbrook Store, and INV-6141 for 1,375.50 and INV-6158 for 690.00 billed to Harbor Street Store. Head office sends one check for 5,755.50 that covers the first three. INV-6158 isn't due yet, so it stays open. Everything is in one subsidiary, US dollars, and one A/R account, with no credits, deposits, or discounts.
01. Check that Consolidated Payments is on
Go to Setup > Company > Enable Features and click the Accounting subtab. Under Advanced Features, Consolidated Payments should be checked. If it isn't, check it and save the page. Without it, a payment only lists invoices for the exact customer named on it, so a parent's check can't close its stores' invoices.
02. Check the parent and its subcustomers
Go to Lists > Relationships > Customers and open Alder Valley Foods. On the Relationships subtab, click Subcustomers. Millbrook Store and Harbor Street Store are listed, each with its own ID, phone, and email. The New Subcustomer button is where you'd add another store.
Click Millbrook Store. Its Parent Company is Alder Valley Foods. That field is the link Consolidated Payments follows. Click Alder Valley Foods in Parent Company to go back to the parent.
03. Read the parent's balances
On Alder Valley Foods, click the Financial subtab and look at Balance Information. Balance is 1,960.00, which is only the parent's own invoice, INV-6120. Consolidated next to it is 6,445.50, the parent and both stores together. With Consolidated Payments on, Overdue Balance, Days Overdue, Deposit Balance, and Unbilled Orders each get a Consolidated amount too, and the aging row is repeated for the whole group.
04. Start the payment from the parent
Go to Transactions > Customers > Accept Customer Payments and choose Alder Valley Foods in Customer. The header shows the same two numbers: Balance 1,960.00 and Consolidated Balance 6,445.50. Check that Date, A/R Account, and Posting Period are what you expect. Here they're 09/24/2026, 1200 Accounts Receivable, and Sep 2026. Undeposited Funds is selected, so the payment waits for a bank deposit. Pick Account instead if you post payments straight to a bank account.
Scroll to the Apply subtab. All four invoices are listed, not just the parent's. Project/Sub is blank on INV-6120, the parent's own invoice, and names the store on the other three: Millbrook Store on INV-6134, and Harbor Street Store on INV-6141 and INV-6158. Their amounts due add up to the 6,445.50 Consolidated Balance. Only open invoices that match the payment's subsidiary, currency, and A/R account are listed, so an invoice in another currency or A/R account won't show up here. If the parent or its stores have open credit memos or deposits, those appear in the Credits and Deposits lists on the Apply subtab and change what's left to apply.
05. Apply the check to the invoices it covers
Type the check total, 5755.50, in Payment Amount. Then check Apply on INV-6120, INV-6134, and INV-6141. Each one's Payment fills with its full amount due: 1,960.00, 2,420.00, and 1,375.50. Leave INV-6158 unchecked. Don't use Pay All or Auto Apply here. They'd also put money on invoices the check doesn't cover, INV-6158 included. Whatever you click, the Summary totals are the thing to check.
Before saving, record how the money came in on the Payment Method subtab, such as Check and the check number. The example leaves it blank. Then scroll back up to the Summary. Applied is 5,755.50 and Unapplied is 0.00, since 1,960.00 + 2,420.00 + 1,375.50 is exactly the check.
06. Save the payment
Click Save. Payment 4417 opens for Alder Valley Foods. Its header now shows Balance 0.00 and Consolidated Balance 690.00. The Apply subtab reads Applied To 5,755.50 and lists INV-6120, INV-6134 with Project/Sub Millbrook Store, and INV-6141 with Project/Sub Harbor Street Store. The payment belongs to the parent, but each invoice stays with the store it was billed to.
07. Check the balances after
Go back to Alder Valley Foods and open the Financial subtab. Balance is 0.00 and Consolidated is 690.00, which is 6,445.50 less the 5,755.50 applied.
Check the result
- The saved payment's Summary reads Unapplied 0.00, and its Apply subtab lists only the invoices the check covered.
- The parent's Balance dropped by the amount applied to its own invoices.
- The parent's Consolidated balance dropped by the full payment.
- Each store's Balance shows only the invoices still open for that store.
On the Relationships subtab, click Harbor Street Store under Subcustomers and open its Financial subtab. Its Balance is 690.00, which is INV-6158, still open for the next payment. Harbor Street Store has no subcustomers of its own, so its Consolidated amount is the same 690.00.
A payment saved to Undeposited Funds still has to go on a bank deposit through your normal deposit process. One posted straight to a bank account doesn't. Either way, saving it doesn't mean the check has cleared or been reconciled.
Common questions
Why don't my subcustomer's invoices show up on the payment?
Check two things. Consolidated Payments has to be enabled, and the parent has to be the customer on the payment. Then the Apply subtab lists open invoices for the parent and its subcustomers, as long as they share the payment's subsidiary, currency, and A/R account. An invoice in another currency or A/R account won't be listed.
What's the difference between Balance and Consolidated Balance?
Balance is what that one customer record owes. Consolidated Balance also includes everything its subcustomers owe. Here, Alder Valley Foods went from Balance 1,960.00 and Consolidated 6,445.50 to Balance 0.00 and Consolidated 690.00, because Harbor Street Store's INV-6158 is still open.
What does the Project/Sub column mean?
It tells you which subcustomer, or project, the invoice was billed to. It's blank on the parent's own invoices. In this example it's how you tell INV-6134 for Millbrook Store apart from INV-6141 for Harbor Street Store, all on one payment.
Does the payment belong to the parent or the stores?
The parent. Payment 4417 is a payment from Alder Valley Foods. The invoices it pays still belong to the stores they were billed to, so each store's own balance drops by what was applied to its invoices: 2,420.00 for Millbrook Store and 1,375.50 for Harbor Street Store.
Can I apply the parent's credit memo or deposit to a subcustomer's invoice?
Yes. With Consolidated Payments on, a payment entered for the parent lists eligible credits and deposits from the whole hierarchy in the Credits and Deposits lists on the Apply subtab. Check the ones you want to use, then apply the amount to eligible invoices on the Apply subtab. This example had no credits or deposits.
Can I still accept a payment directly on a subcustomer?
Usually, yes. You can pick a subcustomer in Customer and pay its invoices the normal way. If the Apply Payments Through Top-Level Customer Only accounting preference is turned on, payments, credits, and deposits have to be applied through the top-level customer instead.