The Ultimate Payroll Checklist for New Payroll Administrators

Starting a new role as a payroll administrator can feel overwhelming—but with the right checklist, you can hit the ground running. Whether you're managing payroll for a small business or joining a large organization, this guide will help you stay compliant, organized, and confident from day one.

✅ Step 1: Understand the Payroll Calendar

Before processing anything, get clear on your company's payroll schedule:

• Pay frequency (weekly, bi-weekly, semi-monthly, or monthly)
• Cut-off dates for timesheet submissions and approvals
• Payday dates
• Deadlines for tax filings and benefits contributions

✅ Step 2: Collect & Verify Employee Information

Ensure you have accurate details for every employee:

• Full legal name, address, and Social Security Number
• Completed W-4 or W-9 forms
• Direct deposit information
• Employment classification (full-time, part-time, contractor)
• State/local tax forms, if applicable

Mistakes here can lead to tax and legal headaches—triple check everything.

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✅ Step 3: Confirm Employee Classification & Exemptions

Misclassifying workers (e.g., contractors vs employees) is one of the most common—and costly—payroll errors. Make sure:

• Each role is properly classified under FLSA (exempt vs non-exempt)
• You understand overtime eligibility and applicable wage laws
• Benefits and deductions are set up accordingly

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✅ Step 4: Set Up Payroll Systems

Depending on the tools your company uses, get familiar with:

• Your payroll software (Gusto, ADP, Paychex, etc.)
• Time-tracking systems
• Any HRIS or ERP integrations

Make sure integrations are working smoothly to avoid manual errors or missing data.

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✅ Step 5: Input Earnings, Deductions & Withholdings

Each pay period, you'll need to account for:

• Base salary or hourly wages
• Overtime and bonuses
• Deductions (benefits, retirement, garnishments)
• Withholdings (federal, state, and local taxes)

Keep an eye on benefit enrollments, changes, and expirations—especially during open enrollment.

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✅ Step 6: Review and Approve Payroll

Before hitting "run payroll":

• Reconcile hours worked vs PTO/sick days
• Double-check new hires, terminations, and raises
• Ensure net pay totals and employer tax liabilities are accurate
• Have a second reviewer, if possible

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✅ Step 7: File and Pay Taxes

Stay compliant with all federal, state, and local tax obligations:

• Deposit payroll taxes (usually monthly or semi-weekly)
• File quarterly payroll tax returns (e.g., Form 941)
• Issue W-2s and 1099s at year-end

Your payroll provider may handle some of these, but you are still ultimately responsible.

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✅ Step 8: Maintain Records & Stay Compliant

Keep payroll records for at least 3–4 years (some states may require longer):

• Paystubs and tax filings
• Time cards and PTO logs
• Employee classifications and wage histories

Stay updated on new labor laws, wage requirements, and compliance deadlines.

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✅ Bonus: Build Relationships with HR & Finance

Payroll doesn’t exist in a vacuum. Sync regularly with HR on new hires, terminations, and benefits—and with Finance on accounting and reporting.

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Wrapping Up

Payroll is one of the most critical functions in any company—you're handling people’s paychecks, after all. This checklist is a great foundation, but every company is different. As you get comfortable in your role, build your own processes, templates, and best practices.

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Need help managing it all?
Consider using a payroll task management tool like Lnkt to stay on top of due dates, documentation, and collaboration with your team. Join our Waitlist at Lnktup.com