Payroll Services Checklist

Reconcile the HRIS roster to the prior pay period. Pull start dates and termination dates from the client's HR system or email; missing terminations create overpayments and missing W-2 corrections later. Note any rate changes or status flips (W-2 to 1099 misclassification is a common audit flag).

I-9 must be completed within 3 business days of start date — Section 2 employer review with original documents. W-4 drives federal withholding; if missing, default to single / no adjustments. State withholding certificate (e.g., NC-4, IT-2104) varies by state. Upload the completed packet to the client portal (TaxDome, SmartVault, Liscio).

Process open-enrollment changes, 401(k) deferral updates, HSA contribution changes, and any new court orders. Garnishments and child-support orders have strict effective dates — late entry creates underwithholding the firm has to cure. Section 125 elections must be in writing before the period begins.

Pull the period's hours from the timekeeping system (When I Work, Homebase, TSheets/QuickBooks Time, ADP Workforce Now). Confirm the pay-period dates match the import — off-by-one-day imports are a recurring source of restated payrolls.

Flag any missed punches back to the client manager — do not guess. Review FLSA overtime: non-exempt employees over 40 hours in a workweek (not pay period) get 1.5x. California requires daily overtime over 8 hours. Tipped employees: confirm tip credit doesn't drop below state minimum.

Generate the preview register before submitting. Spot-check at least three employees: gross-to-net math, 401(k) deferral cap ($23,000 base / $30,500 with catch-up for 2024), HSA family vs. self-only limit, imputed income for group term life over $50K.

Pull the variance report: anything outside ±10% of prior period gross gets investigated. Common causes are bonuses, commissions, retro pay, and missed hours. Don't approve a run with unexplained 30%+ swings — that's how restated payrolls happen.

Email the department manager with the specific employees and dollar swings. Document the response in the run notes. If the variance traces to a system error (duplicate hours, wrong rate), correct in the preview and re-run before approval.

Semiweekly depositors: pay date Wed/Thu/Fri → deposit by following Wed; pay date Sat/Sun/Mon/Tue → deposit by following Fri. Monthly depositors: by the 15th of the next month. Late by 1-5 days = 2% penalty; 6-15 days = 5%; 16+ = 10%. Save the EFTPS confirmation.

State deposit cadences vary widely — CA PIT semiweekly mirrors federal; NY weekly; some states monthly only. SUTA usually quarterly with the wage report. Check each state's portal: e-Services for Business (CA), MyTax Illinois, NCDOR. Multi-state filers should keep a deposit calendar by jurisdiction.

Sum the four 941s for the year and tie wages, SS wages, Medicare wages, and federal withholding to the W-3. Variances over a few dollars require investigation before W-2s go out — SSA reconciliation notices (CP-2100/CP-2100A) trace back to mismatched W-3 vs. 941 totals.

Verify Box 12 codes (D for 401(k), DD for employer health, W for HSA), state-specific boxes, and any third-party sick pay. For 1099-NECs: pull every vendor with $600+ in services, not goods, who returned a W-9 showing non-corporate status. Audit the W-9 file before generation — missing W-9s mean backup withholding exposure.

Tie gross wages, employer taxes, and benefit accruals from the payroll register to the corresponding GL accounts in QBO or Sage Intacct. Variances usually trace to the bank-feed rule miscoding employer-tax withdrawals or to a missing accrual at month-end cutoff.

Document each AJE with a memo, supporting calculation, and reference to the payroll register line. Common entries: accrue mid-period payroll across month-end, reclass employer-paid taxes posted to the wrong account, true up benefit accruals to actual carrier invoices.