Senior Payroll Specialist - Bookkeeper 360

About Bookkeeper360:

NerdWallet, Forbes, and Entrepreneur as a top bookkeeping solution.

We’re proud to be named one of Accounting Today’s 2024 Best Firms to Work For and a Fastest Growing Company by Inc. 5000. With a 4.8-star Google rating from 1,000+ clients, we’re growing fast and expanding our team to meet demand.

About the role:

As a Senior Payroll Specialist, you’ll work with a diverse portfolio of client accounts, supporting 40–60 small businesses across multiple industries and states. You’ll serve as a trusted payroll expert, handling everything from processing and registrations to troubleshooting and platform migrations, ensuring every client’s payroll is accurate, compliant, and on time.

You’ll collaborate closely with our Payroll & HRIS Manager to deliver exceptional client experiences while identifying process improvements that scale.

What you'll do:

Payroll Processing & Compliance

• Process and review multi-state payrolls (weekly, biweekly, semimonthly, and monthly) for a portfolio of 40-60 clients using Gusto, ADP, Paychex, and Justworks, ensuring accuracy, timeliness, and compliance with all deadlines.
• Lead or assist with migrating clients between payroll systems, ensuring accurate data transfers, beginning balances, and compliance alignment.
• Set up and maintain earnings, deductions, reimbursements, and benefits (401(k), HSAs, FSAs, stipends, garnishments).
• Ensure compliance with minimum wage, overtime, and final pay laws across all 50 states.
• Reconcile payroll journals, tax liabilities, and GL postings with accounting teams, ensuring accuracy and timely completion each cycle.
• Identify and correct discrepancies quickly to prevent payroll delays, escalating complex situations when appropriate.

Tax Registrations, Filings & Issue Resolution:

• Coordinate state withholding and unemployment insurance registrations for new employers and handle updates or closures as needed.
• Troubleshoot federal and state payroll tax filings (941, 940, CA DE-9/DE-9C, NY-45, etc.) when filings fail or require intervention.
• Research and assist with amended or prior-period filings (941-X, state amendments, zero filings) under the guidance of the Payroll & HRIS Manager.
• Respond to payroll tax notices or discrepancies, collaborating with agencies or software providers to resolve issues efficiently.
• Maintain an organized database of state registration details, agency credentials, and filing requirements to support departmental consistency.

Client Communication & Collaboration:

• Serve as a primary payroll contact for a large client base, providing clear, timely, and professional communication.
• Work closely with multiple clients simultaneously, ensuring accurate and on-schedule payroll delivery across all accounts.
• Coordinate payroll system transitions by supporting clients through onboarding, data collection, and platform setup.
• Provide expert, approachable guidance on payroll tax, benefits, compliance, and best practices to small business owners and internal teams.
• Collaborate cross-functionally with bookkeeping, tax, and HRIS teams to ensure seamless service delivery.
• Contribute to departmental SOPs, templates, and process improvements to enhance efficiency and scalability.

What Gets You to the Top of the List:

• 5+ years of payroll experience, including multi-state processing and client-facing interaction.
• Hands-on experience registering and maintaining state withholding and unemployment accounts.
• Solid understanding of payroll tax filings (federal and state) and ability to identify and resolve filing discrepancies.
• Working knowledge of labor laws (final pay, overtime, exempt vs. nonexempt, wage theft prevention, etc.).
• Proven ability to manage complex client relationships with professionalism and confidence.
• Adaptability to work across multiple platforms (Gusto, ADP, Paychex, Justworks, Rippling, or similar).
• Strong attention to detail and commitment to compliance.
• Comfort in a remote, fast-paced, client-facing environment.