Guide · 8 min read

    Bookkeeping for nonprofits

    Fund accounting, restricted donations, and Form 990 prep — explained for executive directors who'd rather be running the mission.

    Why nonprofits need fund accounting

    When a donor restricts a gift, you have a legal obligation to spend it on that purpose. A regular P&L can't show that — you need to know, at any moment, how much restricted money is unspent in each fund. That's fund accounting.

    Three fund classes: Unrestricted (operate however you want), Temporarily Restricted (use for a stated purpose or time), Permanently Restricted (endowment — only the earnings can be spent).

    The 4-step nonprofit bookkeeping system

    1. 1

      Set up a nonprofit chart of accounts

      Use the UCOA (Unified Chart of Accounts for Nonprofits) as a starting point. Add income classes for each grant or major donor restriction.

    2. 2

      Tag every transaction with a fund

      Donations land in a specific fund. Expenses are tagged to the fund they draw from. This is non-negotiable — auditors will ask for it.

    3. 3

      Track in-kind donations separately

      Donated services or goods over $5k need to appear on Form 990 Schedule M. Record them at fair market value with a corresponding expense.

    4. 4

      Produce monthly board financials

      Statement of Activities (income & expense by fund), Statement of Financial Position (assets, liabilities, net assets). Boards expect both — every month.

    Expense categories every nonprofit needs

    Program services
    Management & general
    Fundraising
    Staff salaries & benefits
    Contract services
    Occupancy (rent + utilities)
    Insurance
    Office supplies
    Travel & meetings
    Printing & postage
    Professional fees
    Grants paid out

    Books your board will actually read

    SnapBooks tracks restricted funds, generates board financials, and exports Form 990-ready data.

    Start free

    Tools for nonprofit finance

    Frequently asked questions

    How is nonprofit bookkeeping different?+

    Nonprofits use fund accounting — money is tracked by purpose (unrestricted, temporarily restricted, permanently restricted) rather than just income vs expense. A donor who gives $10k for scholarships can't be spent on rent, and your books need to prove that.

    Do I need Form 990?+

    Yes if you're a 501(c)(3). Form 990 (or 990-EZ / 990-N depending on revenue) is due by the 15th day of the 5th month after fiscal year-end. Missing three in a row revokes your tax-exempt status — automatic and brutal.

    How do I track restricted donations?+

    Create a separate income account per restriction: 'Donations — Scholarship Fund', 'Donations — Building Fund'. Expenses against them post to matching expense accounts. Net activity per fund should be on every monthly report.

    Do nonprofits pay any taxes?+

    Generally no federal income tax, but you owe payroll tax on staff, sales tax on most purchases (some states exempt), and UBIT on unrelated business income (e.g. a coffee shop your nonprofit runs).

    What's the simplest nonprofit bookkeeping setup?+

    A chart of accounts with class/fund tagging, monthly bank reconciliation, separate tracking of in-kind donations, and quarterly board financials (Statement of Activities + Statement of Financial Position).