Using the 990 Wizard

Prepare your annual IRS filing data step by step, ready for your tax preparer.

Updated April 1, 2026

The 990 Wizard walks you through preparing your annual IRS filing data step by step. At the end, you get a worksheet to hand to your tax preparer or use to file yourself. The wizard has 7 steps, but most small nonprofits can complete it in 10-15 minutes.

  • Close the accounting period for the fiscal year you're filing. See Closing an Accounting Period. The wizard uses your finalized numbers, so closing first ensures accuracy.
  • Have your officer and board list ready -- names, titles, and hours per week. If officers are already set up in Organization Settings, they'll pre-populate.
  • Review the Form 990 Overview if you're not sure which variant (990-N, 990-EZ, or Full 990) your organization files.

Step 1: Start a new filing

  1. Go to Tax Filing from the sidebar.
  2. Select the fiscal year from the dropdown and click Start Filing.
  3. If you already filed outside NP Ledger (through a preparer or another tool), you can click Mark as Filed Externally instead -- this records the filing for your history without running through the wizard.

Tip: If you have a filing in progress, click Resume in the filing history table to pick up where you left off.

Step 2: Review organization information (Wizard Step 1)

  1. Review your organization's legal name, EIN, address, phone, website, and mission statement. These come from your Organization Settings.
  2. Review the principal officer (the person who signs the return).
  3. Review the officers and directors list. Click Manage in Settings to add or edit officers if the list is incomplete.
  4. If there are compliance gaps (shown as colored warning badges), address them now or note them for later:
  5. Red (critical): Must fix before filing -- like a missing EIN or no officers on file
  6. Orange (high): Strongly recommended -- like a missing address
  7. Yellow (medium): Should review -- like a missing mission statement
  8. Click Save & Continue.

Important: Your EIN (Employer Identification Number) is the 9-digit number the IRS assigned when your organization applied for tax-exempt status. It appears as XX-XXXXXXX. If you don't have it, check your IRS determination letter.

Step 3: Confirm your form variant (Wizard Step 2)

  1. NP Ledger auto-detects which 990 variant you should file based on your gross receipts (total money received) and total assets. The recommendation appears with the supporting numbers.
  2. Review the detection:
  3. 990-N (e-Postcard): Gross receipts normally $50,000 or less (3-year average)
  4. 990-EZ: Gross receipts under $200,000 AND total assets under $500,000
  5. 990 (Full): Gross receipts $200,000+ OR total assets $500,000+
  6. Note your filing deadline and extension deadline shown below the variant.
  7. If you need to file a different variant (rare), expand "I need to file a different variant" and select the correct one.
  8. Click Continue.

Tip: If your organization has fewer than 3 years of data, NP Ledger shows a note that the 990-N threshold is based on limited history. The IRS uses a 3-year rolling average.

Step 4: Review account mapping (Wizard Step 3)

  1. NP Ledger automatically maps your accounts to 990 line items. Review the mapping in two sections:
  2. Part I: Revenue, Expenses, and Changes in Net Assets -- shows each 990 line with the dollar amount and the number of accounts mapped to it
  3. Part II: Balance Sheets -- shows assets, liabilities, and net assets lines
  4. Click any row to expand it and see which specific accounts are mapped there.
  5. Check the status icons on each row:
  6. Green checkmark: mapped and has activity
  7. Orange warning: mapped but shows $0
  8. Red X: negative value or potential issue
  9. If any accounts appear in the Unmapped Accounts section at the bottom, use the dropdown to assign them to the correct 990 line and click Map.
  10. Click Looks Good -- Continue when the mapping is correct.

Step 5: Answer compliance questions (Wizard Step 4)

This is the most detailed step. It covers several sections that correspond to parts of the 990 form.

Program Service Accomplishments: 1. Describe your organization's 3 largest programs -- their names, what they accomplished this year, and their expenses. NP Ledger pre-fills expenses from your program data if available.

Officers, Directors, and Trustees: 1. Review the officer table showing name, title, hours per week, and compensation. Compensation is auto-computed from payroll data when available (marked "Auto"). 2. If any officer earns over $150,000, additional Schedule J questions appear about travel, housing, and severance.

Compliance Questions: 1. Answer yes/no questions about political activities, lobbying, school operations, unrelated business income, and structural changes. Most small nonprofits answer "No" to most of these. 2. Enter the number of voting board members, independent members, employees, and volunteers.

Governance Policies (Part VI): 1. Answer whether your organization has written conflict of interest, whistleblower, and document retention policies. The IRS considers these best practices.

Compensation Process (Part VI, Line 15): 1. Answer whether officer compensation was reviewed by an independent body and based on comparability data.

Board Review (Part VI, Line 11): 1. Confirm whether the board reviews the 990 before filing.

Schedule A -- Public Support Test (for 501(c)(3) organizations): 1. Select your public charity type (most choose the first option). 2. Review the 5-year public support calculation. NP Ledger computes the percentage and shows whether your organization passes the 1/3 support test.

Click Save & Continue when all sections are complete.

Step 6: Review your completed worksheet (Wizard Step 5)

  1. Review all values in the Part I (revenue and expenses) and Part II (balance sheets) tables. Click any row to see the source accounts.
  2. Check the cross-check at the top: Total Revenue minus Total Expenses should equal the Excess/Deficit line. If it doesn't match, review the flagged discrepancy.
  3. Review any schedule summaries that appear:
  4. Schedule B: Major contributors who gave more than $5,000 or 2% of total support
  5. Schedule A: Public support test result (pass, borderline, or fail)
  6. Schedule M: Noncash contributions over $25,000
  7. Schedule G: Fundraising event receipts over $15,000
  8. Schedule J: Officer compensation over $150,000
  9. Address any items needing attention listed at the bottom (severity-coded).
  10. Click Continue to Filing Instructions.

Step 7: Download and file (Wizard Step 6)

If you file 990-N (e-Postcard): 1. NP Ledger shows all the answers you need, with copy-to-clipboard buttons for each field. 2. Go to the IRS website (search for "990-N e-Postcard"), enter the values, and submit. 3. Come back and click I've Filed This Return to record the filing.

If you file 990-EZ or Full 990: 1. Click Finalize & Continue to lock the filing and enable the worksheet download. Once finalized, values can't change. 2. Click Download Worksheet PDF -- this is a line-by-line document matching the official IRS form. 3. Use the worksheet to: - File yourself through a free e-file service like Tax990.com ($40+), or - Hand to your tax preparer -- they transfer the values to the official form 4. After filing, come back and click I've Filed This Return in Step 7.

Step 8: Record the filing (Wizard Step 7)

  1. Verify the filing status shows correctly (Draft, Finalized, or Filed).
  2. If you haven't already, click I've Filed This Return to mark the filing as complete. This records the date for your audit trail.
  3. Click Done to return to the Tax Filing landing page.
  • Line item amounts in Step 5 should match your financial reports (run the Statement of Activities and Statement of Financial Position to compare)
  • All officers are listed with correct compensation
  • All compliance gaps are addressed or acknowledged
  • The cross-check passes (revenue minus expenses equals excess/deficit)
  • Starting the wizard before closing the period. Your numbers may change if the period isn't closed. Close first, then file.
  • Missing officer entries. The IRS requires at least one officer. Add officers in Organization > Settings before starting the wizard.
  • Ignoring account mapping warnings. Unmapped accounts with activity mean that money isn't showing up on the right 990 line.
  • Not exporting the worksheet before marking filed. Once you mark the filing as complete, you can still download, but it's good practice to save a copy first.
  • Confusing "Finalize" with "File." Finalizing locks the worksheet in NP Ledger. Filing means submitting to the IRS. They're separate steps.

Accountant Note: The 990 Wizard generates a preparation worksheet, not the official IRS form. Organizations must file using an IRS-authorized method (e-file via approved transmitter, or paper for qualifying organizations). The worksheet maps directly to Form 990-EZ or Form 990 line items to facilitate accurate transfer. Compensation data follows the reporting requirements of Part VII and Schedule J, using the calendar year ending within the organization's fiscal year.

Ready to try NP Ledger?

Native fund accounting, Form 990 support, and smarter bookkeeping for nonprofits.