How to Set Up and Send Progress Invoices in QuickBooks Desktop
Progress invoicing in QuickBooks Desktop lets you bill an estimate in stages; here is how to switch it on, create the estimate, and invoice parts of it.

A recurring snag for QuickBooks Desktop users is progress invoicing, the ability to split one estimate into a series of partial invoices as work on a job proceeds. The capability exists in Desktop, but it stays off until it is switched on in preferences, and nothing on the invoice form hints at where the setting lives. Users who jump straight from an estimate to the Create Invoice command get a single bill for the full amount and none of the staging choices they expected. The fix is a two-question preference change, after which invoicing from an estimate works the way long-project billing is supposed to work.
What users run into
The complaint takes a predictable shape. An estimate is written for a job that will span weeks or months, and when the first portion comes due, choosing Create Invoice produces an invoice for the entire estimate, with no window asking how much to charge. Some users hunt through invoice templates looking for a progress option and find nothing, because the setting is not on the invoice at all; it lives in company preferences. A second stumbling block appears in multi-user offices: the Company Preferences tab is locked while the file is in multi-user mode, so even users who find the right panel cannot change it until the file is switched to single-user mode.
Turning the feature on
The resolution is short but has prerequisites. Sign in with an administrator account, then use the File menu to switch to single-user mode. Open the Edit menu, choose Preferences, and select Jobs & Estimates from the list on the left. On the Company Preferences tab, answer Yes to the question about creating estimates, then Yes again to the question about progress invoicing directly below it. Choose OK to save, then return to the File menu and switch back to multi-user mode if others need access. The single-user detour is not optional; QuickBooks blocks company-wide preference changes while multiple users are in the file.
Create the estimate that drives the billing
With the preferences set, the work starts in the Customers menu with Create Estimates. Pick the customer, fill in the lines of the job, and save. This estimate becomes the container for the whole project: every progress invoice draws its lines, rates, and running totals from it, so accuracy here prevents corrections later. If you also track costs against jobs, the estimate forms the billing side of the same job costing picture you already keep in Desktop.
The two-choice window
To bill the first portion, open the Customer Center from the Customers menu, select the customer, and open the estimate from their transaction list. With the estimate on screen, choose Create Invoice on the toolbar; the Create Invoice command under the Customers menu works as well. A small window then opens with exactly two choices: create an invoice for the entire estimate, in effect 100 percent, or create an invoice for a percentage of the estimate by typing a percentage into the field provided. Pick one and choose OK. The invoice form opens prefilled with the selected share of the work; verify the amounts, adjust anything that needs adjusting, and save. That invoice is the first in the series.
Billing the balance as work proceeds
Each later billing follows the same route: reopen the estimate and choose Create Invoice again. On these return trips the window works line by line, showing what has already been billed and what remains for each item, so you can bill the remaining amounts, take a further percentage, or select only the items actually delivered so far. Amounts can be fine-tuned per line before saving. Because every invoice stays linked to the estimate, the running totals on the original document reflect cumulative billings without manual updates.
Checking progress across jobs
For an overview, Desktop keeps a report that compares estimates with the invoices drawn against them. Find it under Reports, then Jobs, Time & Mileage, then Job Progress Invoices vs. Estimates. It lays out, per job, how much was estimated, how much has been invoiced to date, and how much is still open, which is usually the fastest way to spot a job whose billing has drifted behind the work.
Where these steps apply
The preference panel and invoicing flow described here are the Windows Desktop ones, common to Pro, Premier, and Enterprise; the screens vary a little between editions and releases, but the Jobs & Estimates preference sits in the same place in each. The enabling step requires an administrator in single-user mode. Once that is done, day-to-day progress invoicing works normally in multi-user mode, and the estimate quietly keeps each job’s billing history tied together from first deposit to final invoice.