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Payment Run: How AP Teams Select, Approve and Release Vendor Payments in an ERP

Sherman Hsieh
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Payment Run: How AP Teams Select, Approve and Release Vendor Payments in an ERP

Last updated: October 13, 2026 · Independent guide · We do not sell rankings or coverage.

A payment run is the scheduled batch in which accounts payable selects approved vendor invoices that are due or discount-eligible, reviews and approves the proposed payments, assigns a payment method, sends a file to the bank, notifies vendors and posts the payments. Most AP teams run it weekly or twice a week. The stages are the same in every ERP, but NetSuite, Microsoft Dynamics 365 Business Central and SAP S/4HANA name the screens differently, and the controls you need sit between those screens.

The payment run in eight stages

  1. Select invoices by due date, discount date and vendor.
  2. Build the payment proposal that groups invoices into payments.
  3. Review the proposal and work the exceptions.
  4. Approve the batch and keep held items out.
  5. Assign the payment method: check, ACH, card or wire.
  6. Generate and release the bank file.
  7. Send remittance advice to vendors.
  8. Post and reconcile the payments.
Stage Responsible Accountable Output
1-2. Selection and proposal AP specialist AP manager Proposal and exception list
3. Review AP manager Controller (consulted on cash) Edited proposal with removal reasons
4. Approval Approvers by threshold Controller or CFO Approved batch and audit trail
5. Payment method Vendor master owner, AP AP manager Payments split by method
6. Bank file and release Treasury or controller Second bank-portal approver Transmitted file, bank confirmation
7. Remittance AP specialist or system AP manager Remittance emails or check stubs
8. Posting Staff accountant Controller Cleared payables, reconciled cash

Adjust the table to your delegation of authority, but keep the person who builds the proposal separate from the person who releases funds at the bank.

1. Select invoices by due date and discount

The AP specialist owns selection. Inputs are approved, matched invoices, the vendor master and the run calendar. Select everything due before the next run date, not only what is due today, or invoices slip a week late. Business Central’s Suggest Vendor Payments batch job has options such as Find Payment Discounts and Summarize per Vendor, and when you enter an available amount it pays prioritized overdue entries first, then other overdue entries, then discount-eligible entries (Microsoft Learn, July 17, 2024).

As an illustration, taking 2/10 net 30 on a $50,000 invoice saves $1,000 for paying 20 days early, an annualized return of about 37% (2/98 × 365/20). A weekly cadence can miss a 10-day window even when cash is available. Our guide to dynamic discounting and early payments in AP software covers sliding-scale programs beyond fixed terms.

What goes wrong: invoices without a due date drop out of date-filtered lists, and unapproved invoices are pulled in because the filter checks status loosely.

2. Build the payment proposal

The proposal is the system’s draft of who gets paid, how much and from which bank account. In SAP S/4HANA, the automatic payment program takes parameters (run date, identification, company codes, payment methods, next payment date); the proposal run then groups open items into payments, assigns methods and bank details, and sends items it cannot resolve to an exception list (SAP Learning, no date shown). In Business Central, the proposal is the set of lines written into the Payment Journal (Microsoft Learn, June 15, 2025). In NetSuite’s Electronic Bank Payments SuiteApp, it is a batch under Payments > Payment Processing > Payment Batch List, where Aggregate by Payee decides whether a vendor’s bills become one payment or several (Oracle NetSuite Help, no date shown).

Controls: build from approved invoices only, save the proposal as first generated, and limit who can create one. What goes wrong: open credits are left out of the selection, so a vendor who owes you a credit receives a full payment.

3. Review the proposal and work the exceptions

The AP manager owns review, and every removal gets a recorded reason. In SAP, clerks can change payment blocks and cash discounts, move items to other payments, or create payments with a different method and house bank (SAP Learning, no date shown). S/4HANA Cloud Public Edition does this in the Manage Automatic Payments and Revise Payment Proposals apps (SAP Learning, no date shown).

Check five things every run: duplicate invoice numbers or amounts, vendors whose bank details changed since the last run, payments far above the vendor’s history, first-time payees, and disputed invoices. Then compare the proposal total with cash in the paying account on the release date. What goes wrong: recurring exceptions are ignored, so the same vendors are paid late by manual check every week.

4. Approvals and holds

Approval confirms that someone with authority, who did not build the proposal, has agreed to release the cash. Holds keep specific invoices or vendors out until a named person releases them.

NetSuite’s Electronic Bank Payments routes a batch for approval when it exceeds the bank account’s payment limit, measured by the largest bill, the largest vendor total or the whole batch, as you choose (Oracle NetSuite Help, no date shown). NetSuite Intelligent Payment Automation, which pays through BILL, has its own payment run approval routing and automatically cancels a payment run that is unresponsive for more than 24 hours (Oracle NetSuite Help, no date shown). Business Central excludes vendor ledger entries marked On Hold from suggested payments (Microsoft Learn, July 17, 2024). SAP payment blocks can sit on the supplier master or the invoice, and whether a block can be removed during the run depends on its configuration (SAP Learning, no date shown).

In the AFP’s 2025 survey, 79% of organizations reported attempted or actual payments fraud in 2024, 63% reported check fraud, and 45% reported vendor impersonation, up 11 points (Association for Financial Professionals, April 15, 2025). Hold any payment to a changed bank account until a call-back to a number already on file confirms it.

5. Assign the payment method

The default comes from the vendor master, and AP confirms or overrides it per payment. In Business Central, electronic payments need a Bank Payment Type of Electronic Payment or Electronic Payment-IAT (Microsoft Learn, August 21, 2025), and Computer Check lines must be printed before the journal can post (Microsoft Learn, June 15, 2025). In SAP, allowed payment methods are a run parameter. NetSuite Intelligent Payment Automation supports check and ACH, plus virtual card, wallet and Mastercard RPPS for vendors on the BILL network (Oracle NetSuite Help, no date shown).

Make sure one bill cannot be paid by two routes: NetSuite notes that its electronic bank payment setting overrides other default payment methods set on entity records, such as vendors, to prevent multiple payment processing (Oracle NetSuite Help, no date shown). Check method limits too: Same Day ACH accepts payments up to $1 million each since March 18, 2022 (Nacha, no date shown), so larger urgent payments need a wire.

6. Generate and release the bank file

The ERP produces the file; the bank moves the money. Business Central exports journal lines with the Export action, and its Credit Transfer Registers page allows re-export after errors, although exported EFT files are not shown there and cannot be re-exported (Microsoft Learn, August 21, 2025). NetSuite’s Electronic Bank Payments creates one file for the selected transactions on the Payment File Administration page, which you download and upload to your bank; it does not transmit files itself (Oracle NetSuite Help, no date shown). SAP creates a payment medium with each successful run, managed in the Manage Payment Media app (SAP Learning, no date shown).

Controls: restrict who can download payment files, compare the file’s count and total with the approved batch before upload, require dual approval in the bank portal, and send a positive pay issue file for every check run. Nacha also requires non-consumer ACH originators to have risk-based procedures to spot unauthorized or false-pretenses entries, effective March 20, 2026 for the largest originators and June 19, 2026 for the rest (Nacha, no date shown). What goes wrong: a file is uploaded twice, or edited on a desktop between export and upload.

7. Send remittance advice

Remittance advice tells the vendor which invoices a payment covers, net of discounts and credits. Without it, vendors misapply cash and chase invoices you already paid. Business Central’s Send Remittance Advice action emails advice from the payment journal or, after posting, from vendor ledger entries (Microsoft Learn, May 2, 2025). NetSuite’s Electronic Bank Payments uses the Email Payment Notification action on the payment file with the Standard Vendor Payment template (Oracle NetSuite Help, no date shown). Under Intelligent Payment Automation, BILL emails the remittance, but discounts you applied appear only in NetSuite (Oracle NetSuite Help, no date shown), so expect questions on short-paid invoices.

8. Post and reconcile

SAP posts payment documents, clears open items and updates the ledgers during the payment run (SAP Learning, no date shown). Business Central documentation describes posting the journal lines once the bank has processed the file (Microsoft Learn, August 21, 2025). NetSuite’s Bill Payment Processing page asks for the posting period in which the payments post (Oracle NetSuite Help, no date shown), so confirm it on runs near month end.

Posting before bank confirmation means a returned ACH leaves a paid invoice the vendor never received; posting after means cash and ledger differ for a day or two. Either works if returns are reversed promptly and the cash account is matched in your cash reconciliation.

Metrics to track

  • On-time payment rate: invoices paid on or before the due date, by vendor.
  • Discount capture rate: discounts taken divided by discounts offered.
  • Exceptions per run: items on the exception list or removed in review, with reasons.
  • Off-cycle payments: urgent payments outside the run, a sign the calendar or approvals are too slow.
  • Returned or rejected payments: ACH returns and voided checks, usually from bad vendor bank data.
  • Cycle time: hours from proposal to bank release.

Our article on AP and AR KPIs and dashboards shows how to track these weekly.

How software supports each stage

Stage NetSuite Business Central SAP S/4HANA
Selection and proposal Pay Bills (core); Bill Payment Processing or Payment Batch List (Electronic Bank Payments); Payment Run (Intelligent Payment Automation) Suggest Vendor Payments into the Payment Journal Automatic payment program (F110); Manage Automatic Payments
Review and holds Edit batch; approval routing On Hold field; edit journal lines Revise Payment Proposals; Manage Payment Blocks
Bank file Payment File Administration Export; Credit Transfer Registers Manage Payment Media
Remittance Email Payment Notification; BILL email Send Remittance Advice Payment advice notes, which can be created during payment medium creation; the SAP Learning lesson on automatic payments does not say how they are sent to vendors

SAP Knowledge Base Article 2858351 ties transaction F110 to the Manage Automatic Payments app (SAP Support, no date shown), and SAP lists an AI-assisted payment exception analysis feature for S/4HANA Cloud Public Edition (SAP, no date shown). NetSuite’s core Transactions > Payables > Pay Bills page pays selected bills directly, and its documentation points to separate custom workflow-based approvals for vendor payments (Oracle NetSuite Help, no date shown), which is why many NetSuite customers add Electronic Bank Payments or Intelligent Payment Automation. Across all three, the usual gaps are vendor bank-detail verification and card payments, which AP automation platforms and bank portals often fill while the ERP keeps posting and clearing payables.

How we researched this

We read the vendor documentation for each stage in Oracle NetSuite Help, Microsoft Learn and SAP Learning, checked Nacha rule pages and the AFP 2025 fraud survey, and reviewed top-ranking pages for “payment run” from Wise (May 18, 2026), Zigaflow (June 24, 2026) and Tacto (no date shown). Those pages describe the steps in general terms but do not name ERP screens, hold mechanics, file controls or posting order; Wise and Zigaflow sell payment or invoicing products. We checked all sources on October 13, 2026.

Related guides

Frequently asked questions

What is a payment run in accounts payable?

A payment run is a scheduled batch in which AP selects due, approved vendor invoices, creates payments, gets the batch approved and sends the payments to the bank. It replaces paying invoices one at a time.

How often should we do a payment run?

Weekly suits most mid-sized companies. Move to twice weekly if you regularly miss 10-day discount windows or make many off-cycle payments, and set the calendar from vendor terms rather than habit.

What is the difference between a payment proposal and a payment run?

The proposal is the editable draft list of payments built from your selection criteria. The payment run, in SAP terms, creates the payment documents, clears open items and posts to the ledger.

Why was an invoice left out of the payment run?

Usual causes are a hold or payment block, an unapproved invoice, a missing due date, missing vendor bank details, or a credit that netted the balance to zero. Check SAP’s exception list, Business Central’s On Hold field, or NetSuite’s due date filters.

Should we post payments before or after the bank confirms them?

Either works if you are consistent. SAP posts during the run, while Business Central documentation describes posting after the bank processes the file. Reverse returned payments quickly and reconcile cash at least weekly.

Sources

Sherman Hsieh

CEO & Editor-in-Chief, Business-Software.com
Independent analysis of enterprise software — ERP, CRM and more
Sherman Hsieh is the founder, CEO, and editor-in-chief of Business-Software.com. He leads the site's independent, buyer-focused coverage of ERP, CRM, and other business systems, including vendor-neutral comparisons, pricing analysis, and implementation guidance. Before founding Business-Software.com, Sherman was an executive at Siebel ...

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