Top 35 Assistant Controller Nonprofit Jobs

Assistant Controller - Behavioral Health
Catholic Charities Serving Central Washington —Yakima, WA
- $95,000 - $105,000 a year
- Full-time
- Microsoft Excel
- Finance
- Analysis skills
- AD&D insurance
- Paid holidays
Accounting Manager/Assistant Controller-Sage Intacct and Bill.com
Cherry Bekaert —Washington, DC
- $120,000 - $135,000 a year
- Hybrid work
- CPA
- Office
- Finance
Quick Apply
Assistant Controller / Director 16803529
Cherry Bekaert —Washington, DC
- $125,000 - $135,000 a year
- Full-time
- Oracle
- Management
- CPA
- Retirement plan
Quick Apply
Assistant Controller / Director
Cherry Bekaert —Washington, DC
- $125,000 - $150,000 a year
- Full-time
- Oracle
- Management
- CPA
- Retirement plan
Quick Apply
Assistant Controller
Episcopal Community Services (ECS) —San Francisco, CA
- $129,637 - $135,471 a year
- Full-time
- CPA
- Current TB test
- Research
Quick Apply
Executive Director - Assistant Controller
Lucile Packard Children's Hospital Stanford —Palo Alto, CA
- $221,000 - $255,000 a year
- Full-time
- Remote
- CPA
- Writing skills
- Research
Assistant Controller
The Morgan Library & Museum —New York, NY
- $115,000 - $130,000 a year
- Full-time
- Writing skills
- Office
- 8 years
Assistant Controller
William & Mary —Virginia
- $130,000 - $150,000 a year
- Full-time
- Remote
- Background check
- CPA
- Customer service
Assistant Treasurer & Controller
New York Institute of Technology —Old Westbury, NY
- $180,000 - $220,000 a year
- Full-time
- Hybrid work
- CPA
- Bachelor of Science
- Research
- Paid holidays
- Paid time off
Assistant Controller
Foodshare Inc —Oxnard, CA
- $100,000 - $130,000 a year
- Full-time
- Management
- CPA
- Office
Quick Apply
Nonprofit CFO (Assistant Vice President).
Hueman PE Talent Solutions —Chicago, IL
- Microsoft Excel
- CPA
- Master's degree
Quick Apply
Assistant Controller
Piedmont Health Services —Chapel Hill, NC
- $111,854 - $150,322 a year
- Full-time
- CPA
- 5 years
- Bachelor of Science
- Paid holidays
- Disability insurance
Quick Apply
Assistant Controller
First Choice Community Healthcare INC —Albuquerque, NM
- Weekends as needed
- Microsoft Word
- Microsoft Access
- CPA
Assistant Controller
NEIGHBORHOOD HEALTH CENTER —Tigard, OR
- $110,468 - $151,893 a year
- Full-time
- Microsoft Excel
- Management
- CPA
- Paid holidays
- Disability insurance
Quick Apply
Assistant Controller - (Senior Accounting Consultant)
Insero & Co. CPAs, LLP —Rochester, NY
- $70,000 - $92,000 a year
- Full-time
- Hybrid work
- CPA
- Mid-level
- Analysis skills
- Paid holidays
- Health insurance
Assistant Controller/Deputy Controller
Osage County Controllers Office —Lyndon, KS
- $25 - $35 an hour
- Full-time
- Hybrid work
- Background check
- Management
- CPA
- Travel reimbursement
- Health savings account
Quick Apply
Assistant Controller
AFRICAN AMERICAN PLANNING COMMISSION INC —Brooklyn, NY
- $100,000 - $120,000 a year
- Full-time
- CPA
- 5 years
- Mid-level
- Commuter assistance
- Paid holidays
Quick Apply
Assistant Controller - Institutional Advancement
Catholic Charities of the Archdiocese of Chicago —Chicago, IL
- $50 an hour
- Background check
- CPA
- 5 years
11d
Assistant Controller - Financial Analysis
Research Foundation of The City University of New York —New York, NY
- $101,292 - $115,000 a year
- Full-time
- Hybrid work
- Bachelor of Science
- Writing skills
- Analysis skills
Director for Accounting and Assistant Controller
The Christian and Missionary Alliance —Reynoldsburg, OH
- $90,000 - $110,000 a year
- Full-time
- 7 years
- Senior level
- Leadership
- Paid jury duty
- Health savings account
4d

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Assistant Controller - Behavioral Health

Catholic Charities Serving Central Washington -
Yakima, WA

Apply Now

Job Details

Full-time
$95,000 - $105,000 a year

Benefits

AD&D insurance
Paid holidays
Disability insurance
Health insurance
Dental insurance
Flexible spending account
Employee assistance program
Vision insurance
403(b)
Life insurance
Prescription drug insurance

Qualifications

Accounting systems
Microsoft Excel
Driver's License
Bachelor's degree
GAAP
Clinical information systems
Accounting and finance experience
Excel data analysis

Full Job Description

Position Summary:

The Assistant Controller – Behavioral Health supports the Agency Controller in overseeing accounting operations, internal controls, compliance, and financial reporting for the agency’s Behavioral Health programs.

This position provides leadership in grant and contract financial management, budgeting, billing, analysis, and funder reporting. The Assistant Controller ensures timely and accurate financial information, assists in the preparation of agency-wide financial statements, and provides financial guidance to program managers and finance staff. This role requires strong accounting expertise, analytical capability, and the ability to manage complex funding structures in a Behavioral Health environment.

Responsibilities:

Accounting & Financial Oversight

Assists the Agency Controller in managing monthly, quarterly, and annual accounting close processes.
Ensures all contract related expenditures align with approved budgets and funding guidelines and proper recording, reconciliation, and reporting of Behavioral Health program revenues, liabilities, and receivables.
Prepares, supervises and reviews journal entries. Reviews account reconciliations, allocations, and billings prepared by accounting staff.
Oversees credit card review for coding, approval and compliance with agency credit card policies. Follows up with staff and managers on any issues.
Monitors payroll to check for accuracy of labor allocations. Follows up with program managers and payroll analyst to verify allocations and ensure needed corrections and updates are made.
Prepares monthly claim liability analysis and reviews with CFO.
Prepares monthly revenue allocation for MCO and GFS revenue.
Prepares and oversees reconciliation between the EHR system and general ledger for Behavioral Health revenues and receivables.
Provides direct program support to Behavioral Health program managers and staff.
Maintains and enhances internal controls over accounting processes and Behavioral Health revenue cycle.
Supports audit preparation (annual audit, federal/state program audits, and funder audits).

Behavioral Health Grants, Contracts & Compliance

Provides advanced oversight of financial management for all Behavioral Health grants and contracts.
Reviews contract terms, reimbursement structures, reporting requirements, and allowable cost guidelines.
Serves as primary financial liaison with funders; interpret compliance rules and communicate financial obligations to leadership.
Oversees preparation and approval of contract and reimbursement billings, claims, and revenue allocations.
Monitors contract performance through return analysis, utilization trends, and budget-to-actual performance.

Budgeting & Financial Planning

Leads the annual budgeting process for Behavioral Health programs in collaboration with the Agency Controller and CFO.
Provides financial modeling, forecasting, and variance analysis for program operations and contracts.
Supports development of budgets for RFPs, contract renewals, and new funding opportunities.
Trains and advises program managers on budget management, allowable costs, and financial policy compliance.

Leadership, Training & Cross-Functional Support

Provides guidance and technical support to accounting staff; serves as point of escalation for complex issues.
Directly supervises one staff Accountant, assigning tasks, reviewing work, coaching, training and supporting professional development. Monitors performance and completes annual evaluation.
Partners with payroll, procurement, operations, and compliance staff to ensure proper labor allocations and contract spending.
Trains Behavioral Health staff on financial policies, documentation standards, and coding requirements.
Represents the Finance Department in EHR user groups and system meetings.

Systems, Reporting & Process Improvement

Maintains accurate financial records, schedules, and audit-ready documentation.
Leads or supports process improvement initiatives to increase accuracy, efficiency, and compliance within accounting operations.
Prepares regular and ad hoc financial reports for leadership, funders, auditors, and program managers.

Perform other duties as assigned

Job Requirements:

The following requirements are those that are normally required for the performance of this position. Any disabled applicant who does not meet one or more of the requirements, but who can perform the essential functions of the job (with or without reasonable accommodations) shall be deemed to meet these requirements.

Physical Requirements:

This position normally requires the physical demands of standing, walking, bending, lifting, or performing other work requiring low physical exertion, talking, and hearing on a regular basis to perform the job requirements. These physical demands are required up to 80% of the time.

Non-Physical Requirements:

Education

Bachelors degree in accounting, finance or related field, required

Experience

5+ years of progressive accounting experience, preferably including grants or contract-based funding, required
Experience in healthcare, behavioral health, medical billing, or insurance billing preferred
Supervisory or lead experience strongly preferred
Experience in contract billing and preparation of budgets is desirable

Special Skills

Strong knowledge of GAAP and non-profit accounting principles
Advanced Excel and proficiency with accounting/EHR systems
Strong analytical, problem-solving, and communication skills
High degree of initiative, accuracy, confidentiality, and attention to detail
Ability to interpret complex billing rules, contract requirements, and compliance guidelines
Excellent verbal and communication skills
Ability to be self-motivated, adaptable to change, and detail- oriented
Ability to work in a team environment
Willingness to take on new responsibilities
Ability to be self-directed and represent the agency in a professional manner

Licensure, Registration, Certification

Valid Washington State driver’s license and required minimum liability insurance for WA State

Employment is conditional upon:

Being cleared by criminal background check and fingerprinting when required

Work Schedule: Monday-Friday, 8:00am - 5:00pm
Wage Range: $95,000-$105,000 per year, depending experience
Benefits:

13 paid holidays, 12 days of vacation, 12 days of sick leave per year
Health insurance including medical & prescription coverage, with optional dental and vision insurance plans. Majority of premiums paid by Catholic Charities
Retirement 403(b) Plan: employee contributions commence upon employment; Catholic Charities contributes 2% of monthly income and matches up to 4% of employee contributions following 6 months of employment
Basic Life Insurance paid 100% by Catholic Charities
Flexible Spending Account eligibility following 6 months of employment
Education Assistance Program reimbursing up to $5,250 per year for approved continuing education after 6 months of employment
Additional voluntary insurances including supplemental life, accidental death & dismemberment (AD&D), critical illness, long term disability, accident, and ID theft
Employee Assistance Program includes 3 counseling sessions per year, legal consultations, financial coaching, and other wellbeing tools
Annual longevity awards begin at 5 years of employment

It is the practice of Catholic Charities to ensure equal employment opportunity without discrimination or harassment on the basis of race, color, national origin, sex, age, disability, citizenship status, marital status, creed, genetic predisposition or carrier status, sexual orientation, gender expression, or any other characteristic protected by applicable law. Applicants from underrepresented backgrounds are encouraged to apply. We gladly offer reasonable accommodations to individuals with disabilities to support participation in the hiring process and employment.

#workforhope

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