Find & Apply For Payroll Manager Jobs in Eden Prairie, Minnesota

We are looking for an experienced Payroll Manager to lead payroll operations for a non-profit organization. This position is ideal for a detail-oriented candidate who can drive accurate, compliant payroll delivery while partnering across HR, Accounting, Benefits, and external vendors. The role will oversee payroll administration, tax compliance, reporting, and system-related activities while supporting a high standard of service, accountability, and continuous improvement.

Responsibilities:

• Direct end-to-end payroll processing across biweekly and semi-monthly cycles, ensuring employees are paid accurately and on schedule.
• Manage payroll compliance activities by enforcing internal policies and aligning processes with federal, state, and local regulations.
• Lead payroll tax administration, including registrations, reconciliations, required filings, and year-end reporting such as W-2 and W-2C preparation.
• Administer payroll system settings and structure, including pay groups, earnings, deductions, and general ledger mappings, while coordinating support and issue resolution with system partners.
• Oversee testing and validation for payroll system updates, enhancements, and related process changes to maintain reliable operations.
• Supervise benefit deduction processing and reconciliation, partnering with Human Resources, vendors, and Accounting to address invoices, funding needs, and payment requests.
• Ensure payroll transactions are accurately reflected in financial records and support month-end, quarter-end, and year-end close activities through reporting and analysis.
• Investigate payroll and accounting variances, prepare audit-ready documentation, and provide reporting for compliance reviews and internal stakeholders.
• Coach and support payroll team members by setting priorities, promoting cross-training, and strengthening a collaborative, service-focused environment.
• Identify opportunities to improve payroll procedures, internal controls, and workflows to increase efficiency, accuracy, and scalability.