At a Glance

Indiana nonprofits must file federal Form 990 (or variations) annually with the IRS, submit Form NP-20R to the Indiana Department of Revenue every five years, and file biennial Business Entity Reports with the Secretary of State. Missing these deadlines can result in penalties, administrative dissolution, or loss of tax-exempt status.

Introduction

Running a nonprofit organization certainly comes with its share of challenges, especially when it comes to staying compliant with various government agencies. While your mission drives your daily work, these annual filing obligations keep your organization legally protected and eligible for tax benefits that are vital to your operations.

Whether you’re managing a small community foundation or a large charitable organization, understanding the complete picture of your filing responsibilities is essential. This guide specifically focuses on the ongoing requirements needed to maintain your nonprofit status—not the initial formation process.

Throughout this article, you’ll discover everything you need to know about federal IRS filings, Indiana Department of Revenue obligations, Secretary of State requirements, and maintaining your tax-exempt status. We’ll break down each requirement into manageable steps, helping you create a compliance calendar that ensures your organization stays on track. When managing multiple state filings or complex reporting schedules, Labyrinth, Inc. helps monitor varying renewal dates, reporting schedules, and jurisdiction-specific rules to keep your organization in good standing.

Federal IRS Filing Requirements

Every tax-exempt organization must file an annual information return or notice with the IRS, unless an exception applies. These filings serve as the IRS’s primary tool for gathering information, educating organizations about tax law requirements, and promoting compliance.

Form 990-N, 990-EZ, 990, and 990-PF explained

The IRS requires different versions of Form 990 based on your organization’s size and type:

• Form 990-N (e-Postcard): A simplified electronic notice for small organizations
• Form 990-EZ: A condensed four-page return for mid-sized organizations
• Form 990: The standard comprehensive return for larger nonprofits
• Form 990-PF: Specifically for private foundations regardless of size

Form 990 not only satisfies federal requirements but also serves multiple purposes. Organizations use it to share information with the public about their programs, and additionally, most states rely on Form 990 to perform charitable oversight and satisfy state income tax filing requirements for organizations claiming exemption.

Who must file which form

The form your nonprofit must file depends primarily on your financial activity:

• Form 990-N: For organizations with gross receipts normally ≤ $50,000
• Form 990-EZ: For organizations with gross receipts < $200,000 and total assets < $500,000
• Form 990: For organizations with gross receipts ≥ $200,000 or total assets ≥ $500,000
• Form 990-PF: Required for all private foundations regardless of financial status

Note that organizations eligible to file simpler forms may voluntarily choose to file more comprehensive returns if desired.

Filing deadlines and penalties

Your annual return is due by the 15th day of the 5th month after your organization’s tax year ends. For example, if your tax year ends December 31, your filing deadline is May 15 of the following year.

For Forms 990, 990-EZ, and 990-PF, you can request an automatic six-month extension by filing Form 8868. However, the Form 990-N deadline cannot be extended, though there is no penalty for late submission.

Failing to file on time carries significant consequences. In general, organizations face a penalty of $20 per day for late filing, with a maximum of the lesser of $10,500 or 5% of gross receipts for the year. For larger organizations, higher per‑day and maximum amounts apply based on annual IRS thresholds. Most importantly, if you fail to file required returns for three consecutive years, your organization will automatically lose its tax-exempt status.

E-filing requirements

Electronic filing is now mandatory for most nonprofit organizations:

• Form 990-N must always be filed electronically
• Forms 990 and 990-PF for tax years ending July 31, 2020 and later must be filed electronically
• Forms 990-EZ for tax years ending July 31, 2021 and later must be filed electronically

Furthermore, as of February 2023, the IRS expanded the electronic filing requirements to include organizations that file at least 10 information returns during a tax year. This includes many common nonprofit filings such as Forms 1099 and employee-related returns.

Electronic filing offers several advantages, including faster processing, fewer errors, and immediate confirmation of receipt. The IRS provides detailed guidance for setting up e-filing through their Modernized e-File system or authorized e-File providers.

Indiana Department of Revenue Filings

Beyond federal requirements, Indiana nonprofits must comply with state-level filing obligations to maintain their tax-exempt status. The Indiana Department of Revenue (DOR) at (317) 232-2240, in.gov/dor, requires several specific filings that differ from your IRS submissions.

Form NP-20R: Five-year compliance report

Beginning in 2023, Indiana replaced the annual NP-20 report with Form NP-20R, which must be filed every five years instead of annually. This represents a significant change for nonprofit compliance in the state.

Your initial filing deadline is assigned by DOR based on the last two digits of your federal employer identification number (FEIN), with initial due dates staggered across 2024–2027. After your initial filing, your organization must file Form NP-20R by May 15 every fifth year. Unlike the previous NP-20, your fiscal year-end date doesn’t affect this schedule—filings are due May 15 of your designated year.

Form NP-20R must be submitted through the Indiana Taxpayer Information Management Engine (INTIME) portal. When filing, you may be asked to provide your most recently completed Form 990 or related documentation as requested by DOR. Failure to file after notice from DOR can result in revocation or cancellation of your exemption. When tracking these complex filing schedules across multiple years, Labyrinth helps organize filing details, reminders, and agency correspondence to ensure you never miss a critical deadline.

Form IT-20NP: Unrelated business income

If your nonprofit earns income from activities not directly related to its mission, you must file Form IT-20NP. The IT-20NP is generally due by the 15th day of the 5th month following your tax year’s end. For instance, if your organization operates on a calendar year, the due date is May 15 of the following year.

Indiana’s corporate adjusted gross income tax rules apply to unrelated business income. Organizations with sufficient liability may need to make estimated income tax payments using Form IT-6. Consult current DOR guidance for thresholds and payment requirements.

Form NP-20A: Sales tax exemption application

To obtain sales tax exemption in Indiana, your nonprofit applies by filing Form NP-20A and following DOR instructions (typically through INTIME). This application generally requires attaching your IRS determination letter confirming your federal tax-exempt status.

Once approved, DOR will provide documentation confirming your nonprofit’s sales tax exemption. Indiana now uses the NP-1 Nonprofit Sales Tax Exemption Certificate generated in INTIME for vendor‑specific purchases.

Renewal process and required documents

Maintaining your tax-exempt status in Indiana requires ongoing compliance. Initially, your organization must complete four essential steps:

1. Register as a nonprofit corporation with the Indiana Secretary of State
2. Obtain tax-exempt status from the IRS (with an FEIN and Form 1023)
3. Register with the DOR by filing Form NP-20A
4. Receive your exemption certificate (Form NP-1) through INTIME

For subsequent renewals, the primary requirement is filing Form NP-20R every five years as mentioned above. The form is relatively straightforward, requiring basic organizational information similar to what was previously reported on NP-20—such as years in existence, organizational mission, and officer information.

Indiana Secretary of State Requirements

Maintaining your nonprofit status in Indiana requires ongoing compliance with Secretary of State filings that differ from your IRS and Department of Revenue obligations. These state-level requirements help ensure your organization remains in good standing and legally authorized to operate.

Business Entity Report: Biennial filing

In contrast to many states requiring annual reports, Indiana nonprofits must file a Business Entity Report with the Indiana Secretary of State (317) 232-6531, inbiz.in.gov, every two years. This biennial requirement begins two years after your initial incorporation date. Your specific filing schedule depends on your formation date—organizations formed in even-numbered years file in even years, while those formed in odd-numbered years file in odd years.

The filing deadline is determined by your anniversary month—the month in which your organization was incorporated. For instance, if your nonprofit was incorporated on March 15, you must submit your Business Entity Report by March 31 every other year. Moreover, you can submit your report up to 90 days before the due date.

First-time filers should note that the initial report comes due in the second year after incorporation and follows the biennial schedule above. For organizations expanding operations or managing multiple state filings, professional compliance management can help track these varying deadlines and ensure timely submission across all jurisdictions. Labyrinth helps nonprofits prepare and submit required state filings—including Annual Reports and Statements of Information—so organizations remain in good standing with state agencies.

Filing methods and fees

The Secretary of State offers two filing methods: online through the INBiz portal or by paper submission. Online filing is recommended as it provides faster processing and fewer errors. A filing fee applies and may vary by filing method; consult INBiz for current amounts and instructions.

Paper filings must include payment payable to the “Secretary of State” and be mailed to the Business Services Division. Filings require basic organizational information including principal address, registered agent details, and names of directors or officers.

Consequences of non-compliance

Failing to file your Business Entity Report can lead to serious repercussions, including administrative dissolution of your nonprofit corporation or revocation of its authority to conduct business in Indiana.

If administratively dissolved, your organization generally cannot conduct business other than actions necessary to wind up its affairs. To pursue reinstatement, you will need to resolve any tax or filing issues (which may include obtaining tax clearance from the Department of Revenue) and file all past-due reports with the Secretary of State.

Maintaining State Tax Exemption

Securing tax exemption is just the beginning—maintaining this status requires ongoing compliance with specific Indiana requirements. To avoid costly penalties or revocation of benefits, your nonprofit must fulfill several critical obligations.

Proof of 501(c)(3) status

Your IRS determination letter serves as the foundation for state tax exemptions in Indiana. This document is typically attached to your Form NP-20A application. Without federal recognition, you cannot qualify for Indiana state tax exemptions.

Once approved, you’ll receive documentation verifying your exempt status with state authorities. This allows you to purchase items without paying sales tax, provided these purchases directly support your nonprofit’s mission.

Using NP-1 with vendors

Indiana uses the NP-1 Nonprofit Sales Tax Exemption Certificate to document sales tax exemption with vendors. To maintain compliance, you generally should:

• Create a separate NP-1 for each vendor through your INTIME account
• Ensure transactions are invoiced directly to your organization
• Verify purchases are used exclusively to carry out your nonprofit’s purpose

Remember that personal purchases for any member’s benefit (meals, lodging, etc.) do not qualify for exemption.

Registered Retail Merchant Certificate (RRMC)

If your nonprofit sells taxable goods or services, Indiana may require a Registered Retail Merchant Certificate. Application, fees, validity, and renewal are administered by DOR; review current DOR guidance to determine whether an RRMC is required for your activities and how to maintain it in good standing.

Altogether, maintaining your tax exemption status requires filing Form NP-20R every five years, with the initial deadline assigned by DOR based on the last two digits of your FEIN. When managing these charitable registration renewals, Labyrinth manages the full renewal process and tracks each deadline to ensure your organization maintains its tax-exempt benefits.

Registered Agent and Recordkeeping Obligations

As part of ongoing compliance requirements, Indiana nonprofits must maintain both a registered agent and proper organizational records. These elements play a crucial role in keeping your organization legally protected.

Why a registered agent is required

Indiana law mandates that every nonprofit maintain a registered agent with a physical street address in the state. This individual or entity serves as your organization’s official point of contact for receiving legal documents, tax notices, and service of process. If your agent fails to receive or forward a legal notice, you might miss court hearings and face default judgments. Currently, P.O. boxes are not acceptable as registered office addresses—only physical locations.

Who can serve as a registered agent

Your nonprofit’s registered agent may be:

• An individual Indiana resident whose business office matches the registered office
• A domestic corporation or nonprofit corporation
• A foreign corporation or nonprofit authorized to transact business in Indiana

Furthermore, commercial agents who file a listing statement with the Secretary of State appear in the state database, simplifying future updates. Despite common practice, appointing yourself as agent limits flexibility since you must remain available during all business hours. Professional registered agent services can provide consistent availability and help manage important compliance notices, particularly when board members or registered addresses change. When updates to officers, directors, or registered agent information become necessary, Labyrinth handles these update filings as part of its corporate filing services.

Keeping bylaws and meeting minutes updated

Regarding recordkeeping, your nonprofit must adopt bylaws before seeking 501(c)(3) status, as the IRS typically requests these during application review. For board meetings, your secretary should document whether each meeting is regular or special, including date, time, location, and attending directors. Ultimately, meeting minutes should record precise wording of proposed actions and resolutions without necessarily including names of those making motions or detailed discussions.

Maintaining accurate corporate records serves multiple purposes beyond IRS requirements. Well-documented meeting minutes protect your organization’s limited liability status, demonstrate proper governance to grantmakers and donors, and provide historical context for future board decisions. We recommend storing these documents electronically with secure backup systems to prevent loss and ensure accessibility when needed for audits or regulatory reviews.

Conclusion

Maintaining compliance with filing requirements stands as a critical responsibility for your Indiana nonprofit. Throughout this guide, we’ve outlined the essential federal and state obligations that protect your organization’s legal status and tax benefits.

Federal IRS filings remain the cornerstone of your compliance strategy. Depending on your organization’s size, you must submit Form 990-N, 990-EZ, 990, or 990-PF by the 15th day of the fifth month after your tax year ends. Missing these deadlines for three consecutive years automatically revokes your tax-exempt status, thus jeopardizing your entire operation.

Similarly, state-level requirements demand your attention. The Indiana Department of Revenue now requires Form NP-20R every five years instead of annually, while the Secretary of State mandates biennial Business Entity Reports. Additionally, organizations with unrelated business income must file Form IT-20NP to report and pay taxes on these activities.

Failure to meet these obligations carries severe consequences. Your nonprofit could face penalties, administrative dissolution, loss of name protection, and inability to conduct business legally. Most importantly, your tax exemptions might be revoked, leading to unexpected tax liabilities that drain resources from your mission-focused activities.

Therefore, creating a comprehensive compliance calendar marks a practical step toward managing these requirements effectively. This approach helps you track deadlines based on your organization’s specific circumstances, such as fiscal year, FEIN number, and incorporation date. For organizations operating in multiple states or managing complex filing schedules, professional compliance management can provide dedicated oversight and deadline tracking to ensure nothing falls through the cracks.

Remember, compliance isn’t just about paperwork—it protects the legal foundation that allows your nonprofit to fulfill its mission. Though these administrative tasks might seem burdensome, they ultimately safeguard your organization’s ability to serve your community and stakeholders without interruption.

Above all, staying informed about changing requirements ensures your nonprofit remains in good standing. The transition from annual to five-year reporting for Form NP-20R and Indiana’s adoption of the NP-1 for sales tax exemption demonstrate how regulations evolve over time. Regular review of your compliance processes consequently helps prevent costly oversights.

Your nonprofit’s important work deserves protection. By following this guide and maintaining proper filing practices, you establish a solid administrative foundation that supports your mission for years to come.

Frequently Asked Questions