Controller (Non-Profit)

Status: Full-Time, Exempt (32 hours/week)
Compensation: $90,000 annually
Location: Hybrid (San Diego County or Imperial County required)

About the Organization

Our client is a mission-driven nonprofit organization with a unique financial and operational structure. In addition to managing a core operating budget of approximately $1.5M, the organization provides fiscal sponsorship to multiple programs and initiatives with combined budgets exceeding $6M.

Financial activities include grantmaking, fiscal sponsorship, and project-based funding that require detailed tracking of restricted and unrestricted funds. Revenue sources include membership dues, grants, and sponsorships, while expenses span operations, payroll, contracts, and programmatic investments.

About the Role

Reporting to senior operations leadership, the Controller plays a critical role in ensuring financial excellence, compliance, and strategic insight. This position blends hands-on financial management with high-level strategic partnership and works closely with executive leadership and the Board’s Finance Committee.

The organization currently utilizes an outsourced bookkeeping partner; the Controller will serve as the primary point of contact and oversee all accounting functions. This is a fully integrated role for a finance leader who enjoys both day-to-day execution and long-term financial strategy in a collaborative nonprofit environment.

Key Responsibilities

Accounting Management (35%)

• Ensure accurate, timely financial reporting in compliance with GAAP, internal controls, and organizational policies

• Lead monthly and annual close processes, including balance sheet reconciliations and functional expense reporting

• Produce financial reports such as P&L, balance sheet, budget vs. actuals, and net asset reports, including visual dashboards

• Manage accounts payable and receivable

• Oversee intercompany transactions between core operations and fiscally sponsored projects

• Serve as primary liaison to outsourced bookkeeping and accounting partners

Financial Management (35%)

• Lead development and ongoing management of the annual budget, clearly distinguishing core and non-core finances

• Analyze financial trends and KPIs to inform strategic decision-making and board-level oversight

• Manage bank and investment accounts and support cash management strategies in partnership with executive leadership

• Oversee payroll and benefits administration in collaboration with People & Culture leadership

• Support grant budgeting, regranting initiatives, and sponsored project financial tracking

• Train and mentor staff on budgeting, financial literacy, and best practices

• Provide financial oversight and reporting for grant-funded and special initiatives

Financial Operations (20%)

• Partner with department leaders to monitor and manage departmental budgets

• Manage banking relationships

• Prepare and coordinate annual audit, Form 990, payroll tax filings, and related compliance reports (W-2s, 1099s, 5500, etc.)

• Serve as staff liaison to audit and finance committees, presenting financial narratives and analysis

• Design, implement, and review internal controls and fiscal procedures

• Evaluate and manage accounting and financial platforms (e.g., QuickBooks Online, expense management tools)
  

Strategic Planning (10%)

• Partner with executive leadership to establish and monitor short- and long-term financial goals

• Provide financial modeling and analysis to support business planning and revenue strategies

This job description is intended to describe the general nature and level of work being performed and is not an exhaustive list of responsibilities.

Qualifications

• Demonstrated experience managing nonprofit finances, including restricted funds and grant budgeting

• Strong background in financial planning, budgeting, forecasting, and financial reporting

• Advanced proficiency in QuickBooks Online and Excel

• Ability to translate complex financial data into clear reports and dashboards for leadership and board audiences

• Experience leading audits and preparing tax filings for similarly sized organizations

• Proven ability to design and implement internal controls and financial processes

• Comfortable working independently while staying closely aligned with organizational goals

• Interest in working within a collaborative, equity-driven, mission-focused organization

• Must reside in San Diego County or Imperial County and be available to work in-office one day per week

Schedule & Work Environment

This organization operates on a four-day work week, with full-time employees working 32 hours per week (Monday–Thursday). Core business hours are 8:30am–5:00pm, with occasional flexibility required to meet deadlines or organizational needs.

The role follows a hybrid work model, with one required in-office day per week and optional office access on other weekdays.

Compensation & Benefits

• $90,000 annual salary

• Generous benefits package including:

• 12 paid vacation days (3 weeks)

• 16 wellness/sick days

• Office closure during the last week of the year

• Medical, dental, and vision insurance

• 403(b) retirement plan with a 5% employer contribution (no employee match required)

• Flexible work hours and hybrid schedule

• Sabbatical, bereavement, and family leave programs

• Employer-provided laptop, technology tools, and software

• Monthly technology stipend