Invoice Processing Checklist
Accounts payable workflow a bookkeeper or AP specialist runs to receive, match, approve, pay, and archive a vendor invoice. Covers three-way match, GL coding, approval routing, payment execution, and 1099 tracking.
Invoice Intake and Verification
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Capture the invoice in the AP inbox
Pull the invoice from Bill.com, Ramp, or the shared ap@ inbox into the working queue. Forwarded PDFs without a vendor name in the file usually need to be renamed before Hubdoc or Dext will route them correctly.
Collects file -
Confirm required invoice fields are present
Required: invoice number, invoice date, vendor remit-to, line-item description, quantity, unit price, total, and tax. Missing invoice number is the most common reason a duplicate-detection rule misfires later.
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Verify a current W-9 is on file
For first payments and at year-end, confirm the W-9 matches the remit-to legal name and TIN. Catching a missing W-9 here — not in January — avoids the scramble before 1099-NEC filing on Jan 31.
Three-Way Match and GL Coding
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Run the three-way match against PO and receiving
Tie the invoice to the purchase order and the receiving report or proof of delivery. Quantities, unit price, and freight terms must match within tolerance. Flag any line that fails as a discrepancy — do not adjust silently.
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Code the invoice to GL account and class
Apply the GL account, class, location, and any project tag in QuickBooks Online or Sage Intacct. If you need a new account to code this, push back — most requests should map to a class or customer dimension, not a new GL account.
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Check for duplicate invoice numbers
Search the vendor record for the invoice number and the dollar amount. Vendors who resend invoices that were never approved are the top source of duplicate payments.
Discrepancy Resolution
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Open a vendor inquiry with the AP contact
Email the vendor's AP contact with the PO number, invoice number, and the specific discrepancy (price, quantity, or freight). Put the invoice on hold in the AP system so it does not pay while disputed.
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Request a credit memo or revised invoice
Specify which is needed — a credit memo against the existing invoice, or a corrected invoice with a new number. Do not let the vendor send a replacement under the same invoice number; it breaks the audit trail.
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Log the dispute in the AP discrepancy register
Record the invoice number, dispute reason, dollar impact, vendor contact, and resolution. The register feeds the monthly AP aging review and the year-end audit PBC list.
Approval Routing
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Route to the budget owner per approval matrix
Send the invoice to the cost-center owner using the approval matrix in Bill.com or Ramp. The approver should see the PO, the receiving report, and the GL coding before they click approve.
Collects list Collects paragraph -
Escalate invoices over $10K to the controller
Per the segregation-of-duties policy, anything over the budget owner's threshold needs a second approval from the controller or CFO. For SOC 1 control environments, the second approval is a key control — do not pay without it.
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Capture the approver signatureCollects signature
Payment Scheduling and Execution
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Schedule the payment per vendor terms
Set the pay date based on Net 30, 2/10 Net 30, or contract terms. Take the early-pay discount when the vendor offers 1% or better — annualized, 2/10 Net 30 is over 36% APR.
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Generate the positive pay file for the check run
Export the check register and upload the positive pay file to the bank before checks hit the mail. Without positive pay, a stolen or altered check clears with no recourse.
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Submit the payment batch in Bill.com
Confirm bank account, debit date, and total before releasing. ACH cutoff is typically 5 PM ET; wires usually 4 PM ET. Friday afternoon submissions for a Monday holiday will not arrive Tuesday.
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Post the payment entry to the GL
The payment should auto-post via the Bill.com sync, but verify the AP clearing account zeroes out and the cash account ties to the bank feed. Stale uncleared payments older than 30 days get flagged at month-end.
Records and Compliance
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Archive the invoice and payment proof in SmartVault
File the invoice, PO, receiving report, approval trail, and remittance advice together. IRS retention is seven years for tax records; many state contracts and audit clauses require longer.
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Update 1099-NEC tracking for the vendor
Confirm the vendor's 1099 flag and YTD reportable total. Services to non-corporate vendors over $600 are reportable on 1099-NEC, due Jan 31. Goods, corporations, and credit-card payments (handled on 1099-K by the processor) are excluded.
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Reconcile the AP sub-ledger to the GL
Run the AP aging and tie it to the GL payables balance. Variances usually trace to a journal entry posted directly to the AP control account — those should be reversed and re-entered through the sub-ledger before close.
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