Not-for-Profit

Accounting & Advisory Services for Nonprofit Organizations

Specialized audit, tax, and financial advisory services for nonprofit organizations across Nebraska and the Midwest.

Nonprofit organizations face increasing scrutiny from donors, grantors, and regulators. Financial transparency, compliance, and strategic stewardship are no longer optional — they are expected. With nearly 350 clients in the not-for-profit sector, HBE’s team of professionals offers the experience and technical skills needed to successfully serve the distinctive needs of clients in this industry. 

At HBE, we provide specialized nonprofit accounting, audit, and tax services to organizations across Nebraska and beyond. From Single Audits to Form 990 preparation and outsourced accounting support, our team understands the unique financial structure of not-for-profit entities.

As a Nebraska CPA firm with deep experience serving nonprofit organizations, HBE understands the financial reporting, audit, and compliance requirements that mission-driven organizations face.

Nonprofit Accounting & Advisory Services

  • Nonprofit financial statement audits
  • Single Audits (Uniform Guidance)
  • Form 990 preparation
  • Outsourced nonprofit accounting
  • Grant compliance support
  • Financial advisory and governance guidance

Nonprofit Organizations We Serve

  • Community foundations
  • Human service organizations
  • Educational institutions
  • Religious organizations
  • Trade and professional associations
  • Government-funded nonprofit organizations

Our Comprehensive Nonprofit Accounting Services

HBE provides a comprehensive range of nonprofit accounting, audit, tax, and advisory services, including the following areas of specialization.

Nonprofit Audit Services

    Nonprofit organizations are entrusted with donor contributions, grant funding, and public resources. Independent audits provide transparency and assurance to boards, funders, and regulatory agencies that financial reporting is accurate and internal controls are functioning effectively.

    HBE provides specialized nonprofit audit services designed to meet regulatory requirements while offering valuable insight into financial operations and governance practices. Our team understands the unique financial structures, reporting standards, and compliance requirements that apply to tax-exempt organizations.

    Our nonprofit audit services include:

    • Financial Statement Audits
      Independent audits performed in accordance with auditing standards to provide assurance that financial statements are fairly presented and comply with nonprofit reporting requirements.

    • Single Audits (Uniform Guidance)
      Audits of organizations that expend federal funding, performed in accordance with Uniform Guidance requirements to ensure proper compliance with federal grant regulations.

    • Grant Compliance Audits
      Evaluating whether grant funds are used appropriately and reported in accordance with program requirements and funding agreements.

    • Internal Control Evaluations
      Reviewing financial processes and internal controls to identify opportunities to strengthen accountability and reduce risk.

    • 403(b) Retirement Plan Audits
      Audits of employee benefit plans sponsored by nonprofit organizations to ensure compliance with ERISA reporting requirements.

    • Board and Governance Communication
      Providing clear communication of audit results and recommendations to leadership and governing boards.

    Our audit approach focuses not only on compliance, but also on helping nonprofit leaders better understand their financial reporting and strengthen organizational oversight.

    HBE provides nonprofit audit and Single Audit services to organizations throughout Nebraska and the Midwest, supporting compliance with federal funding requirements and nonprofit financial reporting standards.

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    Nonprofit Tax Services

    Tax-exempt organizations must navigate complex federal and state reporting requirements while maintaining compliance with IRS regulations governing nonprofit entities. HBE provides specialized nonprofit tax services designed to help organizations protect their tax-exempt status, maintain transparency, and meet reporting obligations with confidence.

    Our team works closely with nonprofit leadership and finance staff to ensure accurate reporting, proactive planning, and clear communication around tax matters that affect mission-driven organizations.

    Our nonprofit tax services include:

    • Form 990 Preparation and Filing
      Preparation of Form 990, 990-EZ, and related schedules to ensure accurate reporting of financial activities, governance practices, and program accomplishments.

    • Unrelated Business Income Tax (UBIT) Analysis
      Identifying and evaluating activities that may generate taxable income and assisting with appropriate reporting and compliance.

    • State and Local Tax Filings
      Assistance with state nonprofit filings, charitable registrations, and other required compliance reporting.

    • Tax-Exempt Status Guidance
      Advising organizations on maintaining IRS tax-exempt status and addressing issues that may arise related to nonprofit operations or structure.

    • IRS Notices and Correspondence Support
      Assisting organizations in responding to IRS inquiries, notices, or examinations related to nonprofit tax filings.

    • Tax Planning for Nonprofit Activities
      Helping organizations understand the tax implications of new programs, partnerships, or revenue-generating activities.

    Our nonprofit tax specialists help organizations remain compliant with IRS regulations while providing clarity around complex tax matters that affect nonprofit operations.

    HBE provides nonprofit tax services to organizations throughout Nebraska and the Midwest, helping mission-driven organizations navigate complex reporting and compliance requirements.

    Outsourced Accounting for Nonprofits

    Many nonprofit organizations need experienced financial leadership but may not require — or have the resources for — a full in-house accounting department. Outsourced accounting provides access to professional financial expertise while allowing leadership teams to remain focused on their mission and programs.

    HBE provides outsourced nonprofit accounting services that support day-to-day financial operations, strengthen reporting processes, and help leadership teams maintain confidence in their financial information.

    Our outsourced accounting services for nonprofits include:

    • Monthly Accounting and Financial Reporting
      Maintaining accurate financial records and preparing timely financial statements that support internal management and board oversight.

    • Budget Development and Monitoring
      Assisting organizations in building realistic budgets and monitoring financial performance against strategic goals.

    • Board-Ready Financial Reporting
      Preparing clear and meaningful financial reports that help board members understand the organization’s financial position and performance.

    • Cash Flow Management
      Helping nonprofit leaders monitor cash flow, plan for funding cycles, and maintain financial stability throughout the year.

    • Grant Tracking and Financial Reporting
      Supporting organizations in tracking restricted funding, managing grant reporting requirements, and maintaining compliance with funding agreements.

    • Controller and CFO-Level Support
      Providing higher-level financial oversight, guidance, and insight to support decision-making and long-term financial planning.

    Our goal is to provide nonprofit organizations with the financial management support and reporting clarity they need to operate confidently, meet compliance requirements, and focus on advancing their mission.

    HBE provides outsourced nonprofit accounting services to organizations throughout Nebraska and the Midwest, helping leadership teams strengthen financial oversight and operational efficiency.

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    Advisory & Strategic Support

    Nonprofit leaders are responsible not only for mission impact, but also for financial stewardship, compliance, and long-term sustainability. Our advisory services help executive directors, finance teams, and boards make informed decisions with confidence.

    HBE works alongside nonprofit leadership to strengthen financial oversight, improve reporting clarity, and support strategic planning that aligns financial resources with organizational goals.

    Our advisory and strategic support services include:

    • Strategic Financial Planning
      Helping leadership evaluate long-term financial sustainability, develop financial projections, and align budgets with mission priorities.
    • Board & Leadership Financial Reporting
      Preparing clear, meaningful financial reports that help boards and leadership teams understand performance, risks, and opportunities.

    • Grant Tracking & Compliance Support
      Establishing processes to properly track grant funding, meet reporting requirements, and ensure compliance with federal and state regulations.

    • Internal Controls & Financial Policies
      Reviewing and strengthening financial procedures to improve accountability, reduce risk, and support strong governance practices.

    • Operational & Financial Process Improvement
      Identifying opportunities to improve accounting workflows, reporting processes, and financial management systems.

    • Organizational Growth & Transition Planning
      Providing guidance as nonprofits expand programs, manage funding changes, or plan for leadership transitions.

    Our goal is to provide nonprofit leaders with the financial insight and guidance needed to support their mission today while building a sustainable organization for the future.

    HBE provides nonprofit financial advisory services to organizations across Nebraska and the Midwest, helping leadership teams strengthen governance, financial oversight, and long-term stability.

    Outsourced Nonprofit Accounting Services
    Advisory & Strategic Support
    • Strategic planning
    • Grant tracking and reporting
    • Internal policy development
    • Risk management
    • Succession Planning

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    Why Nonprofits Choose HBE

    Serving nonprofit organizations throughout Nebrask and the Midwest.

    Deep Nonprofit Industry Experience

    Experienced Single Audit Team

    Partner-Level Accessibility

    Strong Understanding of Grant-Funded Operations

    Regional Presence with Personalized Service

    Frequently Asked Questions

    What accounting services do nonprofits need?

    Nonprofits typically require financial statement audits, Form 990 preparation, grant compliance support, and strong internal controls to meet regulatory and donor requirements.

    When is a Single Audit required?

    Organizations that expend $750,000 or more in federal funds during a fiscal year are generally required to undergo a Single Audit under Uniform Guidance.

    Do small nonprofits need an audit?

    Audit requirements vary based on state law, funding sources, and bylaws.

    Can nonprofits outsource their accounting?

    Yes. Many nonprofits utilize outsourced accounting services to gain CFO-level expertise without hiring full-time staff.

    Financial Clarity. Compliance Confidence. Mission Focus.

    From Lincoln to Omaha and throughout the Midwest, nonprofit organizations rely on strong financial leadership to remain compliant, transparent, and mission-focused.

    Whether your organization requires a Single Audit, Form 990 preparation, or ongoing outsourced accounting support, HBE provides experienced guidance tailored to the nonprofit sector.

    Let’s talk about how we can support your organization’s financial strength and long-term sustainability.

    Connect with our Nonprofit Team