The Payment Run provides a list of approved AP invoices and credit memos with an amount remaining so that an organization can apply credit memos and discounts, create AP payments, print checks, and produce ACH and Positive Pay exports for selected invoices.
With the R365 Payments Service, the Payment Run can also be used to submit payments to R365 Payments, which then delivers payments to vendors using the best available payment method (check, ACH, or virtual credit card) based on the needs of the organization and each vendor.
Payments created through manual payment or the pay bill function on individual invoices will not be processed by the R365 Payments service.
Payments submitted before 5:00 PM Eastern Time (ET) are processed on the same business day. Any payments submitted after 5:00 PM Eastern Time (ET) are processed the next business day.
Security
Payment run permissions are found in the permission tree as follows:
Payment Runs
View Payment Runs
Export ACH in Payment Runs
Send/Edit R365 Payments
Email ACH Stubs in Payment Runs
Print Checks w/Signature in Payment Runs
Print Checks in Payment Runs
Create/Edit Payment Runs
Create Checks in Payment Runs
Approve Payment Runs
Unapprove Payment Runs
Delete Payment Runs
Once R365 Payments has been enabled, any user who previously had permissions to create and approve AP payments can also create payments that use R365 Payments, provided their role includes the relevant Payment Run and AP payment permissions.
These permissions can be added to custom user roles or individual users. The Permission Access report can be used to determine which user roles or users already have these permissions assigned. For more information, see User Setup and Security.
Prerequisites for Paying Vendors with R365 Payments
Before paying vendors with R365 Payments, ensure:
Have complete records, including
General information such as the check name, payment terms, terms discounts, and address.
Payment method configured for R365 Payments (for example, preferred ACH or vCard enrollment).
Are excluded from R365 Payments when necessary.
Are configured and verified for use with R365 Payments, or explicitly excluded when they must not be used with the service.
Have accurate Next Check Number values and any Positive Pay/ACH controls aligned with R365 requirements.
If Positive Pay ACH is enabled with the bank, the organization has added R365’s ACH company ID (1452758311) to the bank’s approved list to prevent delays or rejections for ACH payments.
AP Transactions
AP invoices and AP credit memos are entered and approved so that they appear in the Payment Run grid.
Pay Vendors with R365 Payments
Follow these steps to create a Payment Run that can submit eligible payment through R365 Payments:
Click steps to expand for additional information and images.
1) From the top ribbon, click create then select Payment Run to open a new Payment Run record.
2) Using the Select Invoices From drop-down, select a legal entity for the payment run.
The transactions grid displays invoices and credit memos from locations associated with the selected legal entities.
R365 Best Practice:
It is recommended to create payments for one legal entity at a time.
3) Select the Checking Account that will be used to fund transactions selected in the payment run.
If a default checking account is assigned to the legal entity record, it populates automatically.
The dropdown indicates bank accounts that are enabled for R365 Payments.
Accounts configured for R365 Payments appear under Pay with R365 Payments, while other accounts appear under Pay without R365 Payments.
4) Select the payment Location.
Use the Location dropdown to select the location that will be listed on each payment created in the Payment Run.
If a default location is assigned to the bank account record, it populates automatically.
Selecting a location does not filter which invoices appear in the grid; it controls how payments are labeled.
5) Set the default Payment Date for payments created in this payment run.
This can be adjusted per payment later in the grid.
The date printed on checks generated via R365 Payments reflects the date the payment was sent to the vendor, not just the date entered on the Payment record.
Payments submitted to R365 Payments before 5:00 PM Eastern Time (ET) are processed on the same business day; payments submitted after 5:00 PM ET are processed on the next business day.
6) Review the Next Check Number.
Payments processed through the R365 Payments service show R365 (without a specific number) while in certain statuses, such as:
NotSent
Submitted
Once processing begins and checks are issued, the check number is automatically updated. Reissued checks result in updated payment numbers, which also supports fraud prevention.
If a non-check payment method is used (other than Check or R365 Payments), the Non-Check # sequence and prefix from the Autonumbering page are used, or a generic text label is applied when no sequence exists.
7) Apply filters (vendor groups, location categories, invoice priority) to focus on transactions that should be prioritized for payment. (Optional)
Vendor Group: Select a previously created vendor groups to filter the grid to invoices from that vendors in that vendors group.
Location Reporting Categories: Select one or more previously created location reporting categories to filter the grid to locations in those categories.
Invoice Priority: Filter invoices by their assigned priority (Critical, High, Standard, Low) to optimize cash flow and address the most urgent obligations first.
8) Select transactions in the grid.
Additional grid behavior:
Columns may be filtered or sorted as needed to isolate specific vendors, payment methods, or due dates.
Selected credit memos are automatically applied according to the following sequence:
Invoices with the earliest due date within the same legal entity as the bank account.
If multiple invoices share the same due date, the invoice with the earliest creation date is prioritized.
Remaining invoices in other legal entities, again ordered by due date and then creation date.
If multiple credit memos are included, each is applied in full before the next, in order of credit memo transaction date from oldest to newest.
Payments to the same vendor on the same payment date are combined into one payment unless ‘Payment per Invoice’ is selected on the Vendor record.
Invoices highlighted in orange indicate that one or more line items exceed acceptable variance thresholds, and may warrant additional review.
9) Open the sidesheet to review discounts or update check memos. (if applicable)
After selecting an invoice, use the left arrow above the grid to open the side sheet for that transaction.
The sidesheet displays Check memo and discount details. Proceed to step #12 if updates are needed for these sections. 
10) Update check memos from the sidesheet. (Optional)
In the sidesheet, update or enter the Check Memo:
If a default check memo exists on the Vendor record, it populates automatically.
Any changes to the check memo here update all invoices for the same vendor in the Payment Run that share a payment date.
The check memo is displayed in the description column of the check remittance sent to the vendor.
Check memos entered will update all invoices for the same vendor in the payment run.
11) Review discounts details from the sidesheet. (Optional)
Invoices with available discounts will be indicated with a ‘D’ in column ‘C/D’.
In the sidesheet, review:
Discount Date - This is automatically populated based on the payment term settings and is not editable.
Suggested Discount - If this vendor offers a discount for early payment and the payment days fall within the discount date range, the suggested discount will be listed.
Discount Account - Discounts will be recorded in the discount account that is selected, which is also set on the vendor record. Users also have the option to update this account manually on the payment run.
Discount Taken - This field does not need to be updated unless the value will be different than the suggested value. Discounts are automatically applied when available.
This field is only available to edit if a suggested amount is listed.
12) Review the payments to be created in the payment run in the Payment List Preview tab. (Optional)
13) Save, create, or submit the payment run.
Select one of the following options:
Save the Payment Run
Saves selections and configurations for later editing
Access saved Payment Runs from the Saved Payment Runs dropdown.
Create Payments
Available to users with Create/Edit Payment Runs permissions.
Creates payment records (including those that will be sent to R365 Payments) and opens the Payments created window.
Submit for Approval (if Payment Run approvals are enabled)
Marks the Payment Run as finalized and ready for approval by designated approvers.
The Payment Run moves to Pending status on the Payment Runs page.
It is recommended for approvers to regularly check the payment runs page to review pending approvals.
Organizations with workflows see submitted Payment Runs in nightly workflow emails.
Once payments are created from a Payment Run:
The Payment Run cannot be edited, voided, or deleted as a whole.
Individual payments created from the run can still be edited, voided, or deleted as needed.
14) Select the desired options from the Payments created window.
When Payments created is selected, the Payments Created Window opens.
Review the available options:
Each payment type that applies to the current Payment Run is enabled and can be selected (for example, Print Checks, Export ACH, Send R365 Payments, etc.).
Options that do not apply are grayed out and cannot be selected.
Send R365 Payments must be selected to submit eligible payments to the R365 Payments Service.
If Send R365 Payments (#) is grayed out, one of the following conditions usually applies:
The vendors selected in the Payment Run are not configured to use the R365 Payments payment method.
The Bank Account selected is not set up for R365 Payments.
Payments processed through R365 Payments may initially show R365 in the Payment Number field while they are in statuses such as NotSent or Submitted, and are updated when check numbers are assigned or payments are finalized.