If you bill in stages — for example, a contractor billing 25% at signing, 25% at framing, 25% at drywall, 25% at completion — you have two ways to structure the receivable: progress invoices (multiple smaller invoices issued as work progresses) or one large invoice with partial payments. This article covers the trade-offs and when each pattern is the better fit for your business.
Two ways to bill a job in stages
| Pattern | How it works |
|---|---|
| Progress invoices | Create a separate invoice for each stage as that stage is ready to bill. Each invoice has its own due date and balance. The customer pays each one as it arrives. You collect 100% of each invoice before the next stage ships. |
| One large invoice + partial payments | Create one big invoice for the full job amount, with Allow Partial Payments on. The customer pays portions as work progresses. The invoice stays open with a running balance until the final payment closes it out. |
Why progress invoices are usually better
For most stage-billed jobs, progress invoices win on three dimensions:
- Cleaner A/R aging. A $40,000 invoice that sits at $30,000 balance for three months drags your A/R aging hard. Four $10,000 invoices, each paid within 30 days as the stage completes, keep your aging report healthy.
- Faster cash flow. You're billing for work you can prove was done. Customers pay more promptly when the invoice corresponds to a deliverable they just received, vs. a partial payment on a large open balance they haven't fully consumed yet.
- Easier collections. When a stage invoice goes 30 days late, you have a strong, specific conversation — "we delivered the framing on April 1, the bill is $10,000, please pay." Compared with chasing a partial payment on an open balance, which is squishier.
When one big invoice + partial payments is the better fit
- Your customer's procurement requires one PO per project. Some enterprise customers can only cut one PO for the whole job. Progress invoices break this — they'd each need their own PO.
- The stages aren't well-defined in advance. If you can't predict how the project will be split until you're in it, one open invoice and partial payments is more honest than fabricating stage milestones.
- Very short jobs. If the total job is <$5,000 and finishes in a week, the overhead of multiple invoices isn't worth it.
How both patterns show up in Biller Genie
Biller Genie reflects whatever you set up in your accounting software:
- Progress invoices appear as a series of independent invoices on your Biller Genie invoice grid. Each one has its own reminder cadence, autopay state, and Pay Now link. Each one closes individually as the customer pays.
- One large invoice + partial payments appears as a single invoice with multiple payment entries on the Timeline. Each partial payment reduces the balance until it hits zero. Reminders continue (referencing the remaining balance) until the invoice closes. Requires Allow Partial Payments on the customer's record — see Allowing Partial Payments on Invoices.
Setting up Progress Invoicing in QuickBooks Online
QuickBooks Online has a native Progress Invoicing feature that converts a single estimate into multiple staged invoices. The high-level workflow:
- Turn on Progress Invoicing. In QBO, go to Settings (gear icon) > Account and Settings > Sales. Find the Progress Invoicing section and toggle it on. Save.
- Create an Estimate for the full project total (e.g. $40,000) with detailed line items per stage.
- Issue progress invoices against the estimate as each stage completes. From the estimate, click Create invoice and choose what portion to bill (percentage of total, a specific dollar amount, or specific line items).
- Track remaining estimate balance. QBO automatically subtracts each progress invoice from the estimate's remaining balance, so you always know how much is left to bill.
Each progress invoice syncs into Biller Genie as an independent invoice. They appear with the customer's other invoices in your Biller Genie grid and follow your normal reminder cadence and autopay settings. QBO maintains the parent-estimate relationship; Biller Genie just sees the individual invoices.
For complete QBO instructions (including the Progress Invoice Template setup), Intuit's documentation has step-by-step guides at QuickBooks Support — search "progress invoicing."
QuickBooks Desktop
QBD also supports progress invoicing against an estimate. Enable it under Edit > Preferences > Jobs & Estimates (Company Preferences tab), check "Do You Do Progress Invoicing?" — then create an estimate and use Create Invoice for the Estimate to bill a percentage or amount. Each generated invoice syncs into Biller Genie individually.
Xero
Xero doesn't have a native "progress invoicing against an estimate" feature in the same way. The Xero pattern is to create separate invoices manually for each stage. Quotes can be used as the estimate template, but invoices for each stage are created independently. Each invoice syncs into Biller Genie like any other.
Best practices for stage billing
- Spell out the stages in the original estimate / contract. The customer should already know what stages exist and what each one bills before the first invoice arrives.
- Set due dates that match the stage delivery. Net 15 from "stage delivered" lands better than Net 30 from "estimate signed."
- Don't ship the next stage until the previous one is paid (or paid in part, depending on your policy). This is the main reason progress invoicing improves cash flow — you have a natural gating mechanism.
- Use a memo or invoice description that ties to the stage delivered. "Stage 2 of 4: Framing completed 2026-04-15" beats "Progress payment 2."
- Consider autopay for repeating-stage clients. If you do the same stage rhythm with the same customer repeatedly (monthly retainer plus monthly project work), autopay smooths the cash flow even further.