A grant-funded nonprofit doesn’t just pay people. It has to show which funder paid for each hour, on what basis, with time records and controls a board and a Single Audit can lean on. WageTime allocates a salary across grants and programs at the pay line, carries those segments through to your general ledger, and keeps after-the-fact time records with attestation and locking. It runs for $50 a month plus $10 per person paid that month, with every federal, state, and local tax filed automatically.
US nonprofits employ about 12.8 million people, roughly one in ten private-sector workers, across more than 300,000 establishments, and most of them are small (BLS). That is a business manager and a bookkeeper doing some of the most documentation-heavy payroll there is: split-funded salaries, after-the-fact effort records, and internal controls, all on a fixed grant budget.
Your program director is 40% on the federal grant, 25% on the state contract, 20% on a foundation award, and the rest on unrestricted. Every period, someone rebuilds that split in a spreadsheet, multiplies it out, and re-types the result into payroll and again into the general ledger. Change the percentages and every downstream number has to be redone by hand.
Charge a salary to a federal award and the Uniform Guidance wants after-the-fact records of actual work, not the budget you planned. Personnel costs are the single largest category of disallowed costs in federal grant audits. Right now the “time and effort” behind a grant charge is a memory and a spreadsheet, reconstructed the week the monitor visits.
In a small shop the same person can add the employee, set the direct deposit, approve the run, and reconcile it. That gap is the one auditors flag first: the ACFE’s 2024 fraud study tied more than half of all cases to weak or overridden internal controls, with a $141,000 median loss at organizations under 100 people. A board wants to see approvals, not trust.
Grant budgets are fixed and watched. A per-seat contract that bills for the whole roster in a slow month, or a “call for a quote” payroll price, is hard to defend to a board that reads the functional-expense statement. The headcount that a summer program or a grant cycle swings up and down shouldn’t swing the payroll bill the same way.
The variable-hour roster that crosses the ACA line, the aide’s CPR card that expires next month, staff working in three states, the board report due Thursday, the year-end 1095-Cs. In an office of three, each of those is the finance director’s job after the program day ends.
Each of these gets a real product screen below, shown with sample nonprofit data.
WageTime allocates pay to grants, programs, and funding sources through configurable job-costing segments, so one person’s salary is divided where the work happened instead of in a spreadsheet. Codes run up to 40 alphanumeric characters and adjust to your own grant and program numbering, and the split carries straight through to the general-ledger export. Set a director at 40% federal, 25% state, 20% foundation, and 15% unrestricted, and every paycheck, tax, and benefit line divides on those percentages automatically. When an award closes or a percentage changes, you change it once and every report downstream follows.
| Funding source | Segment code | Percent | Allocated pay |
|---|---|---|---|
| Federal grant Title III | GR-2041 | 40% | $2,600.00 |
| State contract DOA | GR-3110 | 25% | $1,625.00 |
| Foundation award | GR-5507 | 20% | $1,300.00 |
| Unrestricted | UNREST | 15% | $975.00 |
Replaces the allocation spreadsheet, and the second re-keying into the general ledger.
Federal awards want after-the-fact time records that reflect the work actually performed, and WageTime keeps them. Every timesheet carries employee attestation, an audit-ready change log, and locking after approval, so the hours behind a grant charge are documented each cycle instead of reconstructed before a monitoring visit. Staff who split across programs record time to each one, and approved hours flow straight into the payroll run and the allocation. Break and meal rules and rounding options are built in. When a funder asks how a charge was supported, the answer is a report with a signature and a timestamp, not a memory.
| Employee | Program | Hours | Status |
|---|---|---|---|
| Maria O. | Federal Title III | 32.0 | Attested |
| Maria O. | State contract | 20.0 | Attested |
| James T. | Youth program | 40.0 | Attested |
| Dana P. | Food pantry | 28.5 | Change logged |
Replaces the reconstructed time study, and the estimate a monitor won’t accept.
WageTime enforces segregation of duties with role-based access, so the person who enters a change is not the person who approves the run. Approvals are configurable, and every payroll, pay-rate, deduction, and record change is captured in a full audit log with effective dating, so a board or a Single Audit sees who did what and when. Reports run on a schedule and distribute to the finance committee and program managers without anyone exporting and emailing them. The result is the control environment auditors look for in a small finance office, built into payroll instead of promised in a policy binder.
| Action | User | Role | Recorded |
|---|---|---|---|
| Entered pay change | A. Rivera | Preparer | Jul 15, 9:02a |
| Approved payroll run | L. Chen | Finance director | Jul 15, 2:41p |
| Added employee | A. Rivera | Preparer | Jul 12, 11:15a |
| Reviewed & released | Board treasurer | Approver | Jul 15, 3:10p |
Replaces the trust-based approval, and the audit trail nobody could produce.
WageTime runs payroll across sites and programs with department-level controls, division-level overrides, and consolidated reporting, so a multi-program agency sees each program alone or the whole organization together. Run related entities, an affiliated foundation or a separately incorporated program, each under its own EIN with its own filings, all from one login and reported per entity or combined. Finished payroll posts to QuickBooks mapped by department, and a configurable general-ledger export in CSV, IIF, or fixed-width formats feeds the fund-accounting system you already run. The month-end export-and-reformat ritual retires.
| Program | Headcount | Gross pay | Status |
|---|---|---|---|
| Youth services | 14 | $41,280.00 | Posted |
| Senior nutrition | 9 | $23,650.00 | Posted |
| Housing assistance | 6 | $19,900.00 | Posted |
| Administration shared | 4 | $18,420.00 | Allocated |
Replaces the per-program spreadsheet reroll, and the export you reformat by hand every month.
WageTime tracks ACA eligibility for variable-hour and seasonal staff with look-back measurement, hours-of-service, and affordability tracking, then generates and e-files the 1094-C and 1095-C at year-end from payroll data. Weighted-average overtime computes automatically when someone works two programs at two rates in one week. Credentials and licenses, an aide’s CPR card or a case worker’s certification, sit on the employee record with recurring 30, 60, and 90-day expiration alerts. Benefits elections sync to payroll deductions each cycle, and 401(k) administration holds contributions to the annual IRS limits. And because the price is $10 per person actually paid that month, a roster that shrinks between grant cycles shrinks the bill with it.
| Employee | Role | Avg hrs/wk | Status |
|---|---|---|---|
| Dana P. | Food pantry | 28.4 | Under 30 |
| Sam K. | Summer camp | 31.6 | Offer required |
| Priya N. | After-school | 22.0 | Under 30 |
| Marcus L. | Case aide | 29.1 | Monitoring |
Replaces the ACA spreadsheet for seasonal staff, and the payroll bill that ignores your roster.
Set the allocation once as percentages by grant, program, or fund, and WageTime divides that salary, its taxes, and its benefits on those percentages every run. Job-cost codes run up to 40 alphanumeric characters and match your own grant numbering, and the split carries through to the general-ledger export. Change a percentage or close an award and you edit it in one place, not across a spreadsheet and a GL.
Federal awards call for after-the-fact records that reflect the work actually performed, not budgeted estimates, supported by internal controls. WageTime timesheets carry employee attestation, an audit-ready change log, and locking after approval, and staff record time to each program they work. When a funder or monitor asks how a charge was supported, you produce a report with a signature and a timestamp. How the rules apply to your awards is a question for you and your auditor.
501(c)(3) organizations are exempt from federal FUTA tax, and most states still cover them for unemployment while allowing a reimbursable election instead of paying SUTA contributions. WageTime files your state taxes automatically based on how your account is set up. Bring your state and your reimbursable-or-contributory election to the demo and we’ll confirm the exact setup for your organization.
WageTime gives a Single Audit the two things it tests hardest on payroll: documented costs and internal controls. Salaries are allocated to awards with time records that carry attestation and locking behind them, and role-based access plus a full effective-dated audit log show that entry and approval were held by different people. WageTime does not provide audit or legal advice and does not guarantee outcomes, but the control environment auditors look for is built in rather than reconstructed.
Yes. Finished payroll posts to QuickBooks mapped by department, and a configurable general-ledger export in CSV, IIF, or fixed-width formats feeds the fund-accounting system you already run. Tell us your accounting system on the demo and we’ll confirm the exact flow for your setup, including how your grant and program segments map to your chart of accounts.
Yes. Run each program with department-level controls and division-level overrides, and see reporting per program or consolidated across the organization. Related entities, an affiliated foundation or a separately incorporated program, each run under their own EIN with their own filings from the same login, reported separately or combined. Scheduled reports distribute to the board and program managers automatically.
$50 a month for the organization plus $10 per person actually paid that month, with unlimited runs. A summer roster of 40 costs more in July than a winter roster of 18 in January, because you pay for who was paid. Off-cycle runs and corrections cost nothing extra, filings and year-end W-2s and 1099s are included, and there are no long-term contracts. Board-readable, and easy to line up against a grant budget.
One employee whose salary crosses two or more grants, your program and grant codes, and the way you report to funders today. Twenty minutes with a payroll specialist on a live demo organization: you’ll watch a salary allocate across funds, see the time record that documents it, and see the audit log that shows who approved the run.
Book a 20-minute demo