Can You Navigate Certified Payroll in QuickBooks?

QuickBooks can get you started, but certified payroll compliance can quickly become a maze.

QuickBooks Desktop Payroll and QuickBooks Online Payroll Premium and Elite can generate a federal WH-347 spreadsheet, but several fields still require manual entry and a signature. State certified payroll forms and agency uploads, including LCPtracker and California DIR, add more twists and turns.

eBacon gives you a clear path through the certified payroll maze. It handles construction payroll, generates federal WH-347 and state certified payroll reports, prepares agency upload files, and sends a job-costed general ledger file to QuickBooks—all from the same payroll run.

See Certified Payroll built from your own payroll

QuickBooks Desktop Payroll

QuickBooks Desktop Payroll: you set up prevailing wage payroll items, track hours by job, and export a certified payroll report to Excel. A full version of Microsoft Excel is required. Intuit says you can use the report to fill out the WH-347.

QuickBooks Online Payroll Premium and Elite

QuickBooks Online Payroll Premium and Elite (now sold as Intuit QuickBooks Workforce): you set up a project, a weekly pay schedule, and custom pay types, then download a federal WH-347 report as a spreadsheet.

What do you still do by hand when you run certified payroll in QuickBooks?

Quite a bit. Intuit's QuickBooks Online instructions leave you with this whole series of steps you must do manually every week:

Create two custom pay types for every job classification, one for standard time and one for overtime. Intuit suggests putting the wage determination number in each name.
Put every worker on the project on a weekly pay schedule, and enter their hours on weekly timesheets tied to the project.
Enter qualified overtime by hand when you run payroll, if you use custom overtime rates.
Type the project ID, wage determination number, certified payroll number, and apprentice and journey worker details into the report.
Add any cash paid in lieu of fringe, then adjust the totals to match.
Review and sign the Statement of Compliance.

Then, if the job reports to California DIR or LCPtracker, you enter that same payroll again in the portal.

How does eBacon work with QuickBooks?

eBacon takes over payroll, and QuickBooks stays your books. You process payroll once, in eBacon. eBacon then creates a general ledger file built around your own GL codes and job cost structure, ready to download as soon as payroll is done.

QuickBooks Desktop: eBacon syncs job lists and general ledger files automatically within three minutes of a change.
QuickBooks Online: eBacon sends payroll to your books through the GL file.
Your QuickBooks file and chart of accounts stay where they are. If you run QuickBooks Payroll today, payroll moves to eBacon and your accounting doesn't.
A personal implementation manager walks you through setup.

For the details of the accounting connection, see the General Ledger Integration page

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What does eBacon do that QuickBooks wasn't built to do?

eBacon is built for prevailing wage, so the worker’s pay rate matches the report.

eBacon generates the WH-347, the WH-38, the California A-131, and other state certified payroll reports in one click, straight from payroll.
eBacon creates upload files for LCPtracker, California DIR, eMARS, San Diego PRISM, and Washington from the same payroll run, so nobody retypes hours into a portal.
eBacon verifies the wage determination and fringe rate and flags mistakes before they reach a paycheck or a report.
eBacon annualizes fringe credits automatically. For how the bona fide fringe trust works, see the Fringe Benefits page.
eBacon recalculates underpaid wages through restitution and generates updated certified payroll reports, so a mistake doesn't mean rebuilding old reports by hand.
Crews clock in on eBacon's mobile app with GPS, so hours reach payroll without a paper timesheet.

Does eBacon replace QuickBooks?

No. eBacon replaces your payroll provider, including QuickBooks Payroll, not your QuickBooks accounting file. You keep QuickBooks for the books. After every payroll, eBacon creates a general ledger file built around your own GL codes and job cost structure, so payroll lands in QuickBooks without anyone typing it in.

Do I need QuickBooks Online Payroll Premium or Elite to run certified payroll?

For QuickBooks Online, yes. Intuit's certified payroll instructions apply to QuickBooks Online Payroll Premium and Elite, now sold as Intuit QuickBooks Workforce. QuickBooks Desktop users need QuickBooks Desktop Payroll and a full version of Microsoft Excel. Either way, the report covers the federal WH-347 only.

Can QuickBooks send certified payroll to LCPtracker or California DIR?

Unlike QuickBooks, which provides a federal WH-347 spreadsheet but requires manual entry into agency portals, eBacon generates certified payroll upload files directly from the same payroll run for LCPtracker, California DIR, eMARS, San Diego PRISM, and Washington—eliminating duplicate data entry, reducing errors, and simplifying compliance.

Will I lose job-cost detail if I move payroll out of QuickBooks?

No. eBacon builds the general ledger file around your own GL codes and job cost details, so wages land on the right job in QuickBooks and your job cost reports keep the detail you rely on. eBacon's team maps your accounts during setup, so each entry lands where your bookkeeper expects it.

Is a QuickBooks certified payroll report accepted instead of the WH-347?

Yes, it can be. The Department of Labor says use of Form WH-347 is optional, and contractors may submit their payroll on a substitute form as long as it contains the same information and a signed Statement of Compliance. Intuit describes the QuickBooks report as something you can use to fill out the WH-347.

What does switching payroll from QuickBooks to eBacon involve?

Payroll moves to eBacon, and your accounting stays in QuickBooks. A personal implementation manager walks you through setup, including mapping payroll to your chart of accounts so the general ledger file matches how your books work today. Your QuickBooks file, your accountant, and your job cost reports stay where they are.

Book a demo and see yourQuickBooks payroll turned into certified