Common questions about Exempt Organizations in Lacerte

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In this article, you'll find answers to frequently asked questions about Exempt Organizations and Form 990, Form 990-PF, and Form 990-T in Lacerte.

Table of contents:

What forms can be e-filed for Exempt Organization returns (990, 990-T, 4720, states)?

• 990: Main form ✔ | Amended ✔ | Extension/Payment ✔
• 990-T: Main form ✔ | Amended ✘ | Extension/Payment ✔
• FBAR (114): Main form ✔ | Amended ✘ | Extension/Payment ✘
• Form 4720: Main form ✔ | Amended ✔ | Extension/Payment ✔
• California: Main form ✔ | Amended ✔ | Extension/Payment ✘
• Illinois: Main form ✘ | Amended ✘ | Extension/Payment ✘
• New York: Main form ✔ | Amended ✘ | Extension/Payment ✔

When to file?

File Form 990 by the 15th day of the 5th month after the organization’s year end (e.g., May 15 for calendar year). If due date falls on a weekend/holiday, file next business day. 990-series filers can extend 6 months (to November 15 for calendar-year filers). E-files transmitted before local midnight are timely.

How to generate a public disclosure copy for Schedule B?

Lacerte can print a PUBLIC DISCLOSURE COPY of Schedule B:

• Page 1 shows “PUBLIC DISCLOSURE COPY” above the title.
• Other pages omit contributor names/addresses but show contribution data.

Method 1

1. Go to Screen 16.1 – Contributions, Gifts, and Grants.
2. Miscellaneous – Schedule of Contributors section.
3. Check Apply public disclosure copy.

Method 2

1. Settings → Options.
2. Items to Print tab.
3. Set Public Disclosure Copy of Schedule B to Yes.

Additional info

• If neither condition is set, the complete filing copy (with personal info) is generated.
• The Items to Print setting is per return copy (Preparer/Client/Government). Forms view reflects the Preparer Review copy.
• Public Disclosure Copy cannot be e-filed; doing so triggers rejection SB-F990-013 (contributors’ details required).

Why isn’t your SSN/PTIN printing on Form 990 or 990-PF?

Since TY2011, a PTIN is required on all returns. Before 2011, SSN/PTIN/EIN weren’t required unless the org was a section 4947(a)(1) nonexempt charitable trust.

To show the organization is a 4947(a)(1) Nonexempt trust:

1. Go to Screen 1 – Client Information.
2. Return Info section.
3. Check 4947(a)(1) Nonexempt.

You entered the right inputs, but statements aren’t generating on 990/990-PF

Common cause: overrides were entered. Check for:

• Income overrides on Screen 18 – Other Income Producing Activities.
• Expense overrides on Screens 34–46.
• Balance sheet overrides on Screen 50.1.

How do you generate Schedule A?

Schedule A is required only for certain orgs. Any of these will generate it:

Option 1

1. Client Information → Return Info.
2. In 501(c) Paragraph No, select 3 = Charitable, Religious, Educational, Scientific, etc.

Option 2

1. Client Information → Return Info.
2. Check 4947(a)(1) Nonexempt.

Option 3

1. Screen 4.1 – Misc. (990-N, 990, 990-PF, 990-T).
2. Form 990 Miscellaneous section.
3. Check Section 501(e), 501(f), 501(k), or 501(n) org.

To enter Schedule A Part II, line 12 (page 2):

• Screen 52.2 – Support Information → Support information (Schedule A) → Gross receipts from related activities (Part II, Line 12) (Code 52).
  Note: Schedule A Part II generates only if page 1 Part I lines 5, 7, or 8 are checked.

Why can’t I select the first Special Rules box on Schedule B?

Ensure all are true:

• The org is a 501(c)(3) filing Form 990 or 990-EZ.
• On Schedule A Part I (inputs on Screen 52.1 – Public Charity Status), one of these is checked:
  • Line 5: Benefitting a college/university owned/operated by a governmental unit (170(b)(1)(A)(iv))
  • Line 7: Normally receives substantial support from a government unit/general public (170(b)(1)(A)(vi))
  • Line 8: Community trust (170(b)(1)(A)(vi))
• The org passes the 33⅓% support test on Schedule A page 2, line 14.

You entered depreciation on Screen 39—why no Form 4562/special depreciation with 990/990-PF?

Form 4562 isn’t required for 990/990-PF (depreciation is a book deduction). To force Form 4562:

1. Screen 4.1 – Misc. (990-N, 990, 990-PF, 990-T).
2. Under Return Options, check overrides:
   • Form 4562 (990): 1 = yes, 2 = no [O]
   • Form 4562 (990-PF): 1 = yes, 2 = no [O]

Why won’t your Form 990-PF, Part XV fill out?

• Most common: assets did not exceed $5,000 during the year.
• Also complete Screen 43.3 – Grants and Allocations to fill Form 990-PF Part XV (note: source text says “990-XV”).

How do I show that Form 990-PF, column C should be blank?

1. Screen 4.1 – Miscellaneous.
2. Under Form 990-PF → Miscellaneous, check Do not complete Part I col. (c) – Adjusted Net Income (code 38).

How to answer Yes for Form 990 Part VII, question 5?

1. Enter officers in Screen 2 – Officers, Directors, Trustees, Managers.
2. Go to Screen 38.1 – Officers, Directors, Trustees Compensation.
3. Select the applicable officer.
4. Under Form 990 & 990-PF, check Includes compensation from unrelated organizations reportable on Form 990 Part VII and Schedule J.
5. Repeat for each applicable person.

Form 990 Page 3, Part IV, line 4 is blank

• This remains blank until the entity is identified as a Section 501(c)(3).
• If it is a 501(c)(3), indicate this on Screen 1 – Client Information.

Steps:

1. Screen 1 – Client Information → Return Info.
2. Selecting 3 in 501(c) Paragraph no. changes line 4 to No.
3. To change to Yes: Screen 53.1 – Political Campaign & Lobbying Acts (Sch C) → Lobbying Expenditures → enter 1 or 2.

Generating Form 990 or 990-EZ Schedule N – Complete Dissolution of Non-Profit Organization

Lacerte generates Part I or Part II, not both. Per instructions:

• Part I: Organization liquidated/terminated/dissolved and ceased operations (other than winding up).
• Part II: Report significant disposition of net assets (990-EZ see line 36 instructions).

Generate Part I

1. Screen 8.2 – Dissolution or Significant Disposition.
2. Enter Transferred Assets info.
3. Click Miscellaneous.
4. Check applicable boxes, do not check Significant disposition of assets (Part II).

Generate Part II

1. Screen 8.2 – Dissolution or Significant Disposition.
2. Enter Transferred Assets info.
3. Click Miscellaneous.
4. Check Significant disposition of assets (Part II) and any other applicable boxes.

Form 990 Part IX Statement of Functional Expenses – Allocating Expenses

To populate columns B, C, D, enter Allocation Percentages:

1. Screen 34 – Functional Expenses (990).
2. Under Allocation Percentages, enter decimals for:
   • Program services (.xxxx)
   • Management and general (.xxxx)
   • Fundraising (.xxxx)

Lacerte applies these percentages to each expense line. Use override fields in the Expenses section when a line’s allocation differs.

How do you generate Form 990-T?

1. Screen 1 – Client Information.
2. Return Info section.
3. Choose a 990-T Return Type from the dropdown.

Why won’t Form 990-T fill out completely?

Per IRS 990-T instructions:

• If Part I, line 13, column A > $10,000, complete all applicable lines/schedules.
• If ≤ $10,000, complete Part I, lines 1–13, column A; Schedules A–K not required.
• To force full completion: Screen 4.1 – Miscellaneous → Form 990-T Miscellaneous → Complete all parts and schedules.

How to suppress Form 990-T

1. Screen 1 – Client Information → Return Information.
2. Set 990-T Return Type = N/A and 990-T Other Exemption = N/A.

You can’t generate Schedule A Part III on page 4 of Form 990-T—what entries are required?

(To generate Form 990-T, Schedule J):

• Screen 32 – Advertising Income (990-T):
  • Name of periodical
  • 1 = consolidated / 2 = separate (code 1)
  • And at least one of: Gross advertising income (code 2), Direct advertising costs (code 3), Circulation income (code 4), Readership costs (code 5).

Per IRS: if Part I, line 13, column A > $10,000, complete all applicable schedules. If ≤ $10,000, limited completion is allowed. To force Schedule J: Screen 4.1 – Miscellaneous → Form 990-T → Complete all parts and schedules (code 30).

Enter Advertising Income for Schedule A (990-T)

For a schedule to flow to 990-T Page 2, Schedule A – COGS, on Screen 26 – Inventory Sales, enter:

• Business Code (mandatory for 990-T)
• Ending Inventory

When multiple COGS are entered on Screen 26, only the first flows to 990-T

To make a particular schedule flow to 990-T Page 2, Schedule A – COGS, ensure on Screen 26 – Inventory Sales:

• Business Code is entered (mandatory)
• Ending Inventory is entered

Prior year Form 990-T schedules are not generating

(Applies to pre-2020 990-T.) If line 13, column A ≤ $10,000, Schedules A–K won’t generate—only limited parts are required.
To force schedules:

1. Screen 4.1 – Miscellaneous.
2. Form 990-T Miscellaneous subsection.
3. Check Complete all parts and schedules.