Using Bill.com to pay vendor invoices—but not sure how to handle purchase orders?

Bill.com makes it easy to approve and pay bills. But when it comes to managing Bill.com purchase orders, there’s a big gap. You can’t automatically match a PO to an invoice, which means every invoice still needs manual review—even when it’s tied to an approved purchase.

That slows down approvals and creates extra work for your AP team.

Purchase orders are supposed to prevent overspending and speed up invoice processing. With 3-way matching—PO, invoice, and receipt—you can skip manual approvals and close the books faster.

So how do you make purchase orders work in Bill.com without all the manual effort?

This guide walks through three options, including ways to bring full automation, better control, and faster approvals to your existing Bill.com workflow.

Note: ProcureDesk is our system, and we have designed the system to integrate with Bill.com. You can use ProcureDesk for automating purchase to pay processes along with Bill.com. If you are curious about how the system can help you, read more below or

click here to schedule a call with one of our product specialists.

Option 1: Import purchase orders from your accounting system to Bill.com

This is the simplest way to connect Bill.com purchase orders with your accounting system. You create the PO in your account system or ERP—like NetSuite, Sage Intacct, or QuickBooks Desktop—and Bill.com pulls it in for basic tracking.

You can’t do 3-way matching (PO, receipt, invoice). But this setup still supports 2-way matching by linking invoices to approved purchase orders. The idea is to identify an invoice paid against an approved purchase order. However, the invoice must be reviewed and approved before paying the vendor. It works well for basic spend tracking, but not for companies that need budget controls or approval workflows.

Here’s a step-by-step breakdown of how this setup works with Bill.com and your accounting system:

1. Create the purchase order in your accounting system

You’ll start by creating the PO in your accounting software.

⚠️ Note: Bill.com supports purchase order syncing from NetSuite, Sage Intacct, and QuickBooks Desktop (Pro, Premier, Enterprise). It does not support POs from QuickBooks Online or other accounting platforms.

Before creating the PO, your team still needs to follow some sort of approval process. This could be informal—like an email thread—or more structured, using a paper or spreadsheet-based form.

Once approved, someone in the accounting team needs to generate the PO in the accounting system.

Most companies leveraging their accounting system prefer to have one or two people who have access to QuickBooks purchase order functionality.

It creates a bottleneck but is better than opening the accounting system to all users and having compliance issues.

2. Mark the PO as approved in the accounting system

After the PO is created, it may require another layer of approval—depending on your company’s purchasing policy. Make sure the PO is fully approved in the accounting system before it’s sent to the vendor.

3. Sync the PO to Bill.com

Once approved, the PO is automatically pulled into Bill.com during the next sync. The PO number becomes available in Bill.com and can be linked to an incoming invoice.

This lets you track which POs have been billed against. But that’s about the extent of the functionality—there’s no automated matching or budget visibility at this stage.

4. Assign the PO to the invoice in Bill.com

You can manually assign the PO number to an invoice in Bill.com. The rest of your workflow stays the same.

If you’re already reviewing and approving invoices in Bill.com, this integration won’t disrupt that process. You’ll just have a linked PO number to refer to.

Benefits of importing purchase orders to Bill.com

• ✅ Easy to implement – Just enable the native sync with your accounting system
• ✅ Link POs to invoices – Helps you track what’s been billed and paid
• ✅ No major workflow changes – Keep using Bill.com for invoice approvals and payments

Limitations of importing purchase orders to Bill.com

• ❌ Limited integration support – Only works with NetSuite, Sage Intacct, and QuickBooks Desktop (Pro, Premier, Enterprise)
• ❌No 3-way matching – You can’t match POs to receipts and invoices
• ❌ No automation or visibility – POs are static; invoices still need manual approval in Bill.com
• ❌ No real-time spend controls – You can’t catch overbilling or policy violations automatically

When this setup makes sense

This is a good fit if:

• You already manage POs in your accounting system
• You have a low volume of purchase orders
• You don’t need pre-approval workflows or detailed budget controls
• You want to link POs to invoices for tracking, but don’t need deeper automation

Option 2: Create purchase orders and bills in ProcureDesk

ProcureDesk is a complete procurement solution that makes purchase orders work on Bill.com.

Instead of stitching together multiple tools, you can manage everything in one system—requests, purchase orders, invoices, and receipts—before pushing approved bills to Bill.com for payment.

This method enables true three-way matching and eliminates the need to approve every invoice manually. When the match is clean, the invoice is marked as approved and automatically sent to Bill.com in real time.

Employees create purchase requests in ProcureDesk

ProcureDesk makes it easy for employees to submit a purchase requisition and generate POs.

Users can create a PO by:

• Selecting items from internal catalogs
• Manually entering order details
• Using punchout catalogs from preferred vendors like Amazon, Staples, or CDW

With punchout catalogs, employees click a vendor logo (e.g., Amazon), browse the site, and select the items they need. After submitting the request, items are pulled back into ProcureDesk automatically.

ProcureDesk supports over 200+ vendor integrations, giving teams access to real-time pricing and product availability.

Once the cart is ready, the employee clicks “Submit for approval.” That’s it.

No need to guess who should approve the request. The system automatically routes it using pre-configured workflows.

You can set up approval rules based on:

• Dollar amount
• Department or location
• Expense category
• Specific vendors

Automate PO approvals based on custom workflows

With configurable workflows, you can set up the approval process to automatically route the request for approval.

You can set up approval thresholds based on the amount of the purchase request or based on the departments, categories, etc.

The employee doesn’t have to remember where the request should be routed for approval. The employee clicks on the “Submit” button, and the system does the rest.

ProcureDesk gives approvers three ways to review and approve POs:

• Web app – View and act on a full dashboard of pending approvals
• Email – Approve directly from the email without logging in
• Mobile app – Get push notifications and approve requests on the go

This flexibility reduces delays and ensures policies are followed before spending happens.

Convert approved requests into POs and send to vendors

Once approved, the system generates and sends the purchase order to the vendor—no manual steps required.

Vendors receive the PO by email or through cXML if you’re using electronic dispatch.

Here’s a sample of the system-generated PO:

Route invoices into ProcureDesk (not Bill.com)

In this workflow, vendors send invoices to ProcureDesk, not Bill.com.

You can auto-forward your existing AP email inbox so invoices land directly in ProcureDesk for processing.

Once received, invoices appear in your ProcureDesk inbox:

Match invoice to PO and receipt

ProcureDesk reads invoice data using OCR and captures both header and line item details. This eliminates manual data entry.

The system automatically:

• Matches the invoice to the correct purchase order
• Matches line items across both documents
• Confirms the product has been received using the receipt record

This enables true 3-way matching and eliminates the need to manually cross-check multiple documents.

If there’s a perfect match, the invoice is marked “Approved”—no further review needed.

Unlike Bill.com, you don’t need to route matched invoices for manual approval.

Handle exceptions with automated invoice approvals

If there’s a mismatch—like a price discrepancy or missing receipt—ProcureDesk routes the invoice for additional review.

You can also apply invoice approval workflows for:

• Non-PO invoices (like rent or legal services)
• Partial matches where human review is required

Here’s an example of an invoice with a matching exception:

Send matched bills to Bill.com for payment

Once approved, ProcureDesk automatically sends the bill to Bill.com—no need to click a button or wait for a sync cycle.

This includes:

• Invoice header and line items
• Attached invoice file
• Matching details and payment instructions

You’ll see a green checkmark confirming the sync is complete:

Payment and reconciliation through Bill.com

Your AP team can approve and pay vendors using Bill.com, just like before.

Once paid, Bill.com sends the payment status back to ProcureDesk automatically. No need to manually update anything.

Invoices in ProcureDesk are marked “Paid,” and remittance info is recorded:

Benefits of sending bills and purchase orders to Bill.com from ProcureDesk

• ✅ One platform for purchase orders, approvals, invoices, and matching
• ✅ Seamless, real-time integration with Bill.com
• ✅ 3-way match enables auto-approval of clean invoices
• ✅ Reduces manual work and speeds up invoice processing

Cons of sending bills and purchase orders to Bill.com from ProcureDesk

• ❌ If vendors are used to sending invoices directly to Bill.com, they’ll need to change where they send them
• ❌ You’re still using two systems—ProcureDesk for procurement, Bill.com for payments

Option 3: Import bills from Bill.com and match them in ProcureDesk

This workflow is for teams that receive invoices through Bill.com—but still want a proper 3-way matching process to catch errors and enforce compliance.

Instead of starting with a purchase order, this process starts when the vendor sends the bill to your Bill.com inbox. From there, ProcureDesk pulls in the invoice, matches it to the correct PO and receipt, and sends updated invoice data back to Bill.com.

You get control and accuracy—without changing how vendors send invoices or how your AP team pays them.

Start in Bill.com with invoices

Your AP team receives the vendor invoice via the Bill.com inbox. As usual, they create the bill, assign it to the correct chart of accounts, and enter any line item details manually.

Tip: The more accurate your invoice entry is in Bill.com—especially at the line level—the better the match in ProcureDesk.

Here’s what the inbox looks like:

Pull invoices from Bill.com into ProcureDesk

Once the invoice is in Bill.com, ProcureDesk automatically pulls it in. You can schedule this to happen regularly, or manually pull invoices as needed.

The invoice arrives in ProcureDesk ready for validation and matching.

Perform 3-way matching in ProcureDesk

ProcureDesk uses the purchase order number (if present) to start matching the bill to its corresponding PO and receipt. The system displays the results in the invoice matching dashboard:

There are three possible outcomes:

Scenario 1: Perfect 3-way match

If all invoice lines match the PO, and the items have been marked as received, the system completes the 3-way match automatically.

The invoice is marked “Approved” with no manual review required.

Scenario 2: No match found

If the invoice doesn’t have a PO number—or if there’s no corresponding purchase order in the system—your AP team will need to manually match the invoice to the correct PO.

Once linked, the system can complete the 3-way match and approve the invoice (if everything lines up).

Scenario 3: Partial match

Sometimes the invoice only includes a subset of PO line items. Or the descriptions on the invoice don’t exactly match what was ordered.

In these cases, manual review is required to fix the mismatch. This slows down processing time, so it’s helpful to train vendors on how to submit invoices with complete detail.

Update the invoice status in Bill.com

Once the invoice is approved in ProcureDesk, the system sends that approval status back to Bill.com automatically. No need to update it manually.

The invoice now shows as “Approved” in Bill.com and is ready for payment.

Pay using Bill.com

Your AP team continues using Bill.com to approve payments and send funds to vendors—just like they always have.

If you use Bill.com’s internal payment approval process, you can still route bills for one final sign-off before sending payment.

Sync payment status back to ProcureDesk

After the invoice is paid, ProcureDesk automatically updates the invoice status to “Paid.” It also syncs remittance information like payment date and confirmation number.

Here’s how the remittance details appear in ProcureDesk:

Benefits of importing bills from Bill.com and matching them in ProcureDesk

• ✅ No change to your vendor workflow—keep using Bill.com to receive invoices
• ✅ Enables 3-way matching without disrupting your AP process
• ✅ Catch issues early and avoid overpayments
• ✅ Improve invoice accuracy and reduce approval delays

Cons of importing bills from Bill.com and matching them in ProcureDesk

• ❌ Matching can be slower if invoice line items are vague or incomplete
• ❌ Partial data in Bill.com may require more manual intervention
• ❌ Poor invoice formatting makes automated matching harder

What Bill.com’s PO workflow is missing

Bill.com makes it easy to pay vendors. But when it comes to managing purchase orders, there are some key gaps.

If you’re trying to control spend, track budgets, or improve approvals, you’ll likely hit some friction.

Bill.com doesn’t support 3-way matching

You can attach a purchase order to a bill. But Bill.com doesn’t check that the items were received or that the invoice matches the PO.

That means your team has to compare everything manually. It’s easy to miss duplicate charges, incorrect pricing, or billing for things that never showed up.

Approval routing is limited and inflexible

Bill.com does support invoice approvals—but it’s not designed for complex workflows.

You can’t route approvals based on department, project, or vendor. You can’t set rules for who approves what. You also don’t get a full audit trail or status updates for each approval step.

That makes it hard to enforce policy or move quickly.

You don’t get budget visibility or pre-approval

There’s no way to check if a purchase fits within budget before it happens.

Employees can create bills or request payments without seeing how it impacts the spend plan. Finance only finds out after the money’s been committed.

If you need budget controls or pre-approvals, Bill.com alone won’t cut it.

There are no vendor catalogs or punchout options

Bill.com isn’t built for procurement. There’s no way for employees to browse vendor catalogs, compare pricing, or create requests from preferred suppliers.

That means teams go outside the system. They place orders over email or use personal Amazon accounts. And that creates more work for finance to reconcile later.

Managing multiple business entities is manual

If you operate across multiple entities or subsidiaries, Bill.com doesn’t offer strong tools for separating workflows.

You may have to manually manage different approval processes, user roles, or vendor lists for each entity. That slows things down and increases the chance of error.

Why teams add ProcureDesk to Bill.com

Bill.com is built for handling payments. But most growing finance teams need more than just invoice approvals and ACH transfers.

They need to manage what happens before the invoice shows up.

ProcureDesk fills that gap in financial operations. It helps you control spending, enforce policies, and streamline approvals—without changing how you pay vendors in Bill.com.

Automate approvals and stay compliant

With ProcureDesk, you can build approval workflows that match how your business works.

Want to route any request over $2,500 to the department head? Done. Need IT to review all software purchases? Easy.

Approvers get notified by email, mobile, or inside the app. And they don’t have to log in to approve—just click from their email. Everything is tracked and time-stamped.

For example, if someone submits a $7,000 request for marketing swag, it might go to the team lead, then the VP of marketing. You don’t have to chase anyone—ProcureDesk handles it.

Get real-time budget visibility before spending happens

Employees see what’s left in their budget before they hit submit.

If the marketing team has $10,000 left for events, and someone tries to request $12,000, they’ll see that red flag instantly. So will their manager.

You can track budgets by department, GL code, project, or custom fields. Finance gets visibility without digging through spreadsheets or emails.

Match POs, invoices, and receipts without manual work

ProcureDesk handles 3-way matching automatically.

When an invoice is received, the system checks it against the PO and the goods receipt. If everything matches—same price, same quantity—it’s marked ready for payment.

No human review needed.

If there’s a mismatch, like a $5 overcharge or missing item receipt, ProcureDesk flags it. You only step in when something needs fixing.

This saves hours each week and cuts down on payment delays.

Scale your AP process without hiring

Let’s say you’re processing 200 purchase orders a month across three departments. Without automation, that means dozens of approval emails, lots of status follow-ups, and manual matching for every invoice.

ProcureDesk simplifies all of it.

You don’t need to hire another AP specialist just to keep up. You get more control, fewer errors, and faster processing—while still paying vendors through Bill.com like you always have.

This not only improves efficiency—it also protects your cash flow by preventing late payments, duplicate bills, or missed approvals.

Get white-glove onboarding with zero setup stress

Don’t have time to build custom workflows? We’ll do it for you.

ProcureDesk offers 100% done-for-you onboarding. Our team sets up everything—approval rules, punchout catalogs, budget tracking, invoice matching, and your Bill.com integration.

We learn how your current purchasing and AP processes work, then automate all of it.

Most customers are up and running in 2–3 weeks, with no extra work for the finance team.

Whether you’re moving from paper forms or trying to clean up messy email approvals, we’ll handle the heavy lifting so you can hit the ground running.

FAQ about purchase orders in Bill.com

Can I use Bill.com for procurement?

Sort of. Bill.com has recently launched a lightweight purchase requisition feature that lets you submit purchase requests, get approvals, and send purchase orders. But it’s still limited.

You won’t get:

• Full budget visibility before approval
• Advanced approval routing by department or location
• Support for punchout catalogs or vendor selection
• Advanced 3-way matching with receipts
• Multi-entity workflow management

So while Bill.com is building more procurement features, it’s still focused on AP and payments. If you need full control over spending before the invoice shows up, you’ll still want to pair it with a tool like ProcureDesk.

Note: As of writing this article, Bill’s requisition feature is not available to all users

Can Bill.com support multiple companies?

Yes, but it’s manual. You can manage multiple companies or entities under one login, but each has its own workflow. You’ll need to switch between them and set up separate vendors, approval rules, and chart of accounts for each one.

If you’re handling multiple legal entities, departments, or business units, it can get messy fast.

Does Bill.com support 3-way matching?

No. Bill.com doesn’t support automated 3-way matching between purchase orders, invoices, and receipts.

You can attach a PO number to a bill, but it won’t check if the items were received or if the invoice details match the original PO. Matching has to be done manually or outside of Bill.com.

What’s the difference between a purchase order and a bill in Bill.com?

A purchase order is a document you send to a vendor that confirms what you want to buy, how much, and at what price.

A bill (or invoice) is what the vendor sends back when they want to get paid.

Bill.com is focused on processing bills—not creating or managing purchase orders. You can attach a PO to a bill, but you can’t create or approve POs inside Bill.com.

How does ProcureDesk integrate with Bill.com?

ProcureDesk connects directly to Bill.com to sync approved invoices.

Once a purchase request is approved and the invoice is matched to the PO and receipt, ProcureDesk sends the bill to Bill.com automatically. That includes the full invoice data, line items, and attachments.

Your AP team can keep using Bill.com to approve and pay bills—just with cleaner, pre-approved data that doesn’t need extra validation.

Final thoughts: choose the PO workflow that fits your growth

Bill.com works well for payments. But it’s not designed to manage the full purchase order process.

If your team just needs to link a PO to an invoice, importing POs from your accounting system might be enough.

For small businesses that rely on Bill.com, ProcureDesk adds the control and automation missing from basic PO workflows. If you need tighter control—like approvals, budget checks, and 3-way matching—ProcureDesk can do the heavy lifting while still letting you pay vendors through Bill.com.

Whether you’re growing fast or just tired of chasing approvals over email, ProcureDesk gives you the structure and automation to scale without hiring more people.

We’ll even set it up for you. In just 2–3 weeks, your entire purchasing and AP process can run on autopilot.

Get a free demo of ProcureDesk today and see how easy it is to take control of spend—before the invoice ever hits your inbox.