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Automating invoice reconciliation means letting software capture each supplier invoice, compare it with the purchase order (PO) and, where needed, the goods receipt, and pass clean matches through. Anything that fails a rule goes to a named person. The software does the matching. You still have to set the rules, supply usable PO and receipt data, and decide who handles mismatches.
The workflow at a glance
- Map where invoices, POs and receipts live, and which system is authoritative.
- Capture invoice data in structured form.
- Choose a matching method per invoice type.
- Set tolerances and validation rules.
- Auto-accept clean matches and route exceptions.
- Lock down review and audit evidence.
- Measure results against a baseline.
Step 1: Map the process and the system of record
Before configuring anything, list where invoices arrive (email, supplier portal, EDI, paper), where POs and receipt confirmations are stored, and which ERP or accounting system is authoritative. Then decide the scope: PO-backed invoices, non-PO invoices, or both. PO matching does not cover invoices that have no PO, such as utilities or professional services. Those need a separate coding and approval route.
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Step 2: Capture invoice data
For digital invoices, define one structured intake route, such as a dedicated mailbox, portal or e-invoicing feed, so every invoice enters the same pipeline. Paper invoices need a digitization step. Microsoft’s Dynamics 365 documentation describes paper invoices being processed through OCR, either by third parties or through its Invoice capture service.
If you still receive meaningful paper volume, a document scanner feeding your OCR tool is the supporting hardware for this step. Microsoft’s documentation doesn’t endorse any scanner brand or model. Businesses whose invoices are already digital don’t need one.
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Capture is not reconciliation. Extracted fields still have to be matched and validated against your records.
Step 3: Choose the matching method
Microsoft Learn’s Dynamics 365 Finance guide defines the three-way match this way: “The invoice net unit price is compared to the purchase order’s net unit price and the matching product receipt quantity is compared to the invoice quantity.” A two-way match drops the receipt comparison.
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| Method | What is compared | When it fits |
|---|---|---|
| Two-way line match | Invoice line price against PO line price | PO-to-invoice comparison is the control requirement and receipt confirmation isn’t part of it. |
| Three-way line match | Invoice price against PO price, plus invoice quantity against received quantity | You need proof that invoiced goods arrived and receipt records are available. |
| Invoice-total match | Selected invoice totals against PO totals, within configured variance limits | Totals are an acceptable validation level. It gives less detail than line-level checks. |
| Charges or price-total matching | Charges, or cumulative line amounts across invoices, against the matching PO amounts | Charges need separate validation, or suppliers issue several invoices against one PO line. |
These modes are documented for Dynamics 365. Other platforms use different names and options, so check your own product.
Receipt data is the usual blocker for three-way matching
Three-way matching only works if receipts exist in the system. SAP Concur’s setup instructions, for example, require quantity receipt data to be imported by file or API, or entered in its receiving workflow. If warehouse or service receipts are patchy, start with two-way matching and add receipt matching once the data is dependable. Otherwise you will generate false exceptions.
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Step 4: Set tolerance and validation rules
Tolerances decide whether a difference is flagged or tolerated. Dynamics 365 compares discrepancies against configured tolerances for line-level, invoice-total, charges and price-total matching. Its documentation notes that, depending on configuration, a discrepancy may need approval before posting or may be allowed with a warning.
- Set price and quantity tolerances from your own policy and risk appetite. There is no universal percentage or amount.
- Add totals checks (lines plus tax and charges equal the invoice total).
- Define vendor- or item-specific exceptions, for example bulk commodities with variable weights.
- Treat product defaults as starting points only. SAP Ariba, for instance, documents a default validation-skip threshold of 5 in the site’s default currency. That is a configuration default, not a recommended threshold.
Step 5: Auto-process the routine, route the rest
The aim is that invoices meeting the rules move on without a person touching them, and every failure lands with someone accountable. SAP Ariba describes automatic reconciliation as matching invoice documents and lines to orders or contracts, then deciding whether to validate, skip validation, accept, reject, or send the invoice to exception handlers or approvers.
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Give each common exception type an owner and a route:
- Price variance beyond tolerance: purchasing or the buyer.
- Quantity invoiced exceeds quantity received, or no receipt: the receiving team or requester.
- No matching PO: route to the non-PO approval process, or return to the supplier.
- Capture or validation failure: AP staff correct the data or request a corrected invoice.
Step 6: Preserve controls and audit evidence
These are recommendations drawn from the approval, tolerance and exception controls these products document. They are not a universal configuration. Decide in advance:
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- who may amend source data such as PO prices or receipts, and who may resolve exceptions (keep these separate where practical);
- what evidence must be attached to a resolution, such as a supplier credit note or a receiving note;
- which invoices may post without human review, and up to what value.
Step 7: Measure your own results
The official product documentation reviewed (Dynamics 365, SAP Ariba, Sage Intacct) doesn’t give independent, comparable benchmarks for accuracy, time savings or cost savings. Don’t expect a promised figure. Record a baseline before go-live, then track:
- share of invoices matched without intervention;
- exception volume, split by cause;
- time spent waiting for receipts or approvals;
- how often matched invoices are later corrected;
- time from receipt to posting.
Exception causes tell you what to fix next. Many are upstream issues, such as late receipts or stale PO prices, rather than tolerance problems.
Use your ERP or add a tool?
Dynamics 365, SAP Ariba, SAP Concur and Sage Intacct all document relevant matching capabilities. If your ERP already covers your match type, tolerances and exception routing, configure it first. If it doesn’t, compare add-on AP automation tools on matching coverage, tolerance controls, receipt-data handling, exception workflow, approval options and integration with your accounting system.
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