At a Glance

Nebraska nonprofits must complete both federal IRS Form 990 filings annually and state biennial reports every odd-numbered year. The federal Form 990 deadline is the 15th day of the 5th month after your fiscal year ends, while the Nebraska biennial report is due by April 1 in odd-numbered years (2023, 2025, 2027, etc.).

Introduction

Unfortunately, many Nebraska nonprofits lose their tax-exempt status each year simply because they missed critical filing deadlines. Your mission is too important to be derailed by paperwork oversights. Maintaining compliance isn’t just about checking boxes—it’s about protecting the very foundation that allows your nonprofit to serve its community.

Fortunately, staying compliant in Nebraska doesn’t have to be overwhelming. From federal Form 990 submissions to Nebraska’s biennial reports and maintaining proper tax exemptions, each requirement follows a predictable schedule you can plan for. Labyrinth, Inc. helps nonprofits prepare and submit required state filings—including annual reports and statements of information—so organizations remain in good standing with state agencies.

This step-by-step guide breaks down exactly what you need to file, when to file it, and how to avoid common pitfalls that trip up even established organizations. By the end, you’ll have a clear roadmap to confidently manage your nonprofit’s ongoing filing obligations and keep your focus where it belongs—on your mission.

Federal Filing: IRS Form 990 Requirements

All Nebraska nonprofit organizations must fulfill IRS annual reporting requirements to maintain their tax-exempt status. These federal filings provide transparency about your organization’s finances and operations while confirming your continued eligibility for tax exemption.

Which Form 990 to file: 990-N, 990-EZ, 990, or 990-PF

The version of Form 990 your nonprofit must file depends primarily on your annual gross receipts and total assets:

• Form 990-N (e-Postcard): For organizations with gross receipts normally $50,000 or less, as outlined in the IRS Form 990-N e-Postcard guidance. This simplest version requires just eight basic information items about your organization.
• Form 990-EZ: For organizations with gross receipts less than $200,000 and total assets less than $500,000, per the IRS Form 990 series filing thresholds. Despite the “EZ” designation, this form still requires detailed financial information and can run 4–15 pages depending on your organization’s complexity.
• Form 990: Required for organizations with gross receipts $200,000 or more, or total assets $500,000 or more, according to the IRS Form 990 series filing thresholds. This comprehensive form can reach up to 50 pages and requires extensive financial and operational details.
• Form 990-PF: Required for all private foundations regardless of financial status; see the IRS Form 990 series overview.

Notably, churches are exempt from Form 990 filing requirements under the IRS rules on automatic revocation and filing. Additionally, organizations eligible for simpler forms may voluntarily file more detailed versions if preferred; see the IRS 990-N filing guidance.

Filing deadlines and extensions

Your Form 990 is due on the 15th day of the 5th month after your fiscal year ends, per the IRS annual return due date guidance. For example:

• Calendar year ending December 31: Form due May 15
• Fiscal year ending June 30: Form due November 15

Should the deadline fall on a weekend or legal holiday, it automatically extends to the next business day, according to the IRS due date rules.

Most forms can receive an automatic six-month extension by filing Form 8868 before your original due date, as described in the IRS extension guidance. This moves your deadline to:

• Calendar year filers: November 15
• June 30 fiscal year end: May 15 the following year

Form 990-N filers should note that while extensions aren’t available for the e-Postcard, there’s no penalty for late submission unless it’s your third consecutive missed filing; see the IRS 990-N e-Postcard page.

However, failing to file any required 990 form for three consecutive years will automatically revoke your organization’s tax-exempt status, per the IRS automatic revocation rules. This revocation happens on the due date of the third missed year, creating significant consequences for your ability to operate as a nonprofit.

Where and how to file

The IRS has moved toward electronic filing for Form 990 submissions:

• Form 990-N must be filed electronically through the IRS website and requires a Login.gov or ID.me account for access to the e-Postcard system, per the IRS 990-N e-Postcard guidance.
• Forms 990, 990-EZ, and 990-PF are filed electronically using an IRS-authorized e-file provider; creating an IRS Login.gov or ID.me account is not required to submit these returns, as noted in the IRS Form 990 series guidance.

The Form 990 serves multiple purposes beyond IRS compliance. It’s a public document accessible to potential donors and watchdog agencies. Many states also rely on Form 990 information for state-level oversight and tax exemption verification.

For the smoothest filing experience, gather all required documentation before starting, including financial statements, board member information, and program accomplishment details. Following the detailed instructions for your specific form will help ensure your nonprofit maintains good standing with federal authorities.

State Filing: Nebraska Biennial Report

Beyond federal IRS requirements, Nebraska nonprofits must comply with state-specific filing obligations to maintain their legal status. The Nebraska Biennial Report is a crucial filing that ensures your nonprofit remains in good standing with state authorities.

Who must file and when

All domestic and foreign nonprofit corporations operating in Nebraska must file a biennial report with the Secretary of State, as required by Nebraska statute 21-19,172. Unlike some other entity types, nonprofits in Nebraska follow an odd-year filing schedule; see the Nebraska Secretary of State annual/biennial reporting guidance. The biennial report must be submitted between January 1 and April 1 of odd-numbered years (2023, 2025, 2027, etc.), per Nebraska statute 21-19,172.

Specifically, your first biennial report becomes due in the first odd-numbered year following your nonprofit’s formation, according to Nebraska statute 21-19,172. For instance, if you formed your nonprofit in 2023 or 2024, your first report would be due by April 1, 2025.

The official due date is April 1, and filings not received by the delinquency date of June 16 are subject to administrative action, as noted by the Secretary of State’s biennial reporting page. When necessary, we will track these renewal dates and manage deadline reminders so organizations can focus on their mission rather than compliance details.

Filing fees and methods

You can submit your biennial report online via the Secretary of State’s eDelivery portal or by paper to the address listed on the form; see the annual/biennial reporting information. Nebraska charges filing fees that vary by filing type and method; consult the Nebraska Secretary of State forms and fee information for current fees and any applicable online service charges.

To access the online or paper filing options, you’ll need your nonprofit’s Secretary of State identification number. This information can be found on prior correspondence or by searching your organization’s name on the Secretary of State’s website.

Furthermore, the biennial report must include specific information such as:

• Your nonprofit’s name and state/country of incorporation
• Registered office address and current registered agent
• Principal office street address
• Names and addresses of directors/principal officers
• Brief description of activities
• Whether the organization has members
• Whether it is a public benefit, mutual benefit, or religious corporation, as described in Nebraska statute 21-19,172

Consequences of missing the deadline

Failure to file your biennial report by the June delinquency date carries serious consequences. The Secretary of State may administratively dissolve your nonprofit corporation, according to the biennial reporting guidance. Once dissolved, your organization loses its legal standing in Nebraska and faces significant limitations.

If your corporation is administratively dissolved, you may apply for reinstatement by filing the appropriate forms with the Secretary of State’s Business Services Division. The standard reinstatement filing fee is $30, and late reinstatement carries a substantially higher fee of $500, per the forms and fee schedule.

Administrative dissolution impacts more than just paperwork—it affects your nonprofit’s ability to conduct business, access courts, and maintain the liability protections afforded by your corporate structure. Consequently, staying current with biennial reporting requirements is essential to your organization’s operational continuity. Labyrinth tracks these critical deadlines and ensures timely submission to maintain good standing.

Nebraska State Tax Exemptions

Maintaining proper tax exemptions represents a key aspect of your nonprofit annual filing requirements in Nebraska. Understanding which exemptions apply to your organization—and what you need to do to keep them—can save you substantial resources.

Corporate income tax exemption rules

Nebraska generally recognizes federal income tax exemption for organizations that are exempt under section 501(c) of the Internal Revenue Code. In practice, this means most such organizations do not file a Nebraska corporate income tax return unless they have unrelated business taxable income. If your organization has unrelated business income, you may need to file the appropriate Nebraska return in addition to any federal filing.

Sales tax exemption eligibility

Conversely, sales and use tax exemptions in Nebraska work differently. The mere fact that your organization is nonprofit does not automatically qualify you for sales tax exemption. In fact, most nonprofit organizations must pay sales tax on purchases unless they fall into specific categories, as outlined in the Nebraska Department of Revenue nonprofit tax exemptions guide.

Organizations eligible for sales tax exemption include:

• Religious organizations created exclusively for religious purposes
• Nonprofit organizations providing services exclusively to the blind
• Nonprofit Nebraska-licensed hospitals and health clinics
• Nonprofit educational institutions established under Nebraska statutes
• Nonprofit licensed residential child-caring agencies
• Nonprofit mental health and substance use treatment centers (among other specified categories), per the Department of Revenue guidance

To claim this exemption, apply to the Nebraska Department of Revenue (commonly using Form 4, Nebraska Exemption Application for Sales and Use Tax). Once approved, present your exemption certificate number to sellers using Form 13 (Nebraska Resale or Exempt Sale Certificate) when making qualifying tax-exempt purchases, as detailed in the nonprofit tax exemptions guide.

Unrelated business income considerations

Even though your nonprofit enjoys tax exemption, you may still have filing obligations related to unrelated business taxable income (UBTI). When your organization generates income from activities unrelated to your exempt purpose, that income remains subject to taxation, per the IRS unrelated business income tax overview.

If your nonprofit has $1,000 or more of gross unrelated business income, you must file federal Form 990-T. You may also need to file a Nebraska corporate or fiduciary income tax return (for example, Form 1120N for corporations or Form 1041N for trusts), as applicable; see the IRS UBIT guidance.

Property tax exemption presents another consideration. Nonprofit organizations seeking property tax exemption should file with the County Assessor by the statutory deadline (generally by December 31 of the year preceding the exemption period), and must provide the information required by law to support the exemption.

Remember that maintaining your tax exemptions requires consistent attention to filing deadlines and accurate reporting. Missing these requirements could result in unexpected tax liabilities that divert resources from your mission.

Maintaining a Registered Agent in Nebraska

As part of your ongoing nonprofit annual filing requirements, Nebraska law mandates that every nonprofit corporation maintain a registered agent within the state. This critical compliance element ensures your organization remains in good standing with state authorities.

Why a registered agent is required

Nebraska statutes explicitly require all nonprofit corporations to continuously maintain a registered agent in the state; see Nebraska statute 21-1934. The registered agent serves as your organization’s official point of contact for receiving legal documents and official government communications. Most importantly, this individual or entity accepts service of process if your nonprofit faces litigation.

Failing to maintain a proper registered agent carries serious consequences. The Nebraska Secretary of State can administratively dissolve your nonprofit corporation if you don’t fulfill this requirement. Once dissolved, you’ll need to file for reinstatement and pay applicable fees. Moreover, without a certificate of good standing during this period, your organization may face operational limitations.

Who can serve as a registered agent

Nebraska law provides flexibility regarding who can serve as your nonprofit’s registered agent. According to state statutes, your registered agent may be:

• An individual Nebraska resident whose business office matches the registered office address, per Nebraska statute 21-1934
• A domestic business or nonprofit corporation with an office identical to the registered office, per Nebraska statute 21-1934
• A foreign business or nonprofit corporation authorized to conduct business in Nebraska with an identical office, per Nebraska statute 21-1934

The registered agent must maintain a physical street address in Nebraska—post office boxes alone are insufficient, per Nebraska statute 21-1934.

While board members or employees can serve as registered agents, many nonprofits opt for professional registered agent services to ensure consistent availability and maintain privacy.

How to update agent information

Keeping your registered agent information current remains vital to your nonprofit’s annual compliance requirements. Should your registered agent change or relocate, you must promptly notify the Nebraska Secretary of State by filing a “Change of Registered Agent and/or Office” form.

For nonprofit corporations, the filing fee to change registered agent/office is $30 in-office or $25 online, and filing can be completed through the Secretary of State’s online portal or by mailing the completed form; see the Nebraska forms and fee information.

Maintaining accurate agent information helps ensure you receive any official notices related to biennial reporting and other compliance matters. Labyrinth handles these update filings as part of its corporate filing services when organizations need to update their registered agent information.

Other Ongoing Compliance Requirements

Proper documentation forms the foundation of your nonprofit’s compliance strategy beyond just filing reports. Several additional requirements merit your attention throughout the year.

Keeping nonprofit records up to date

The IRS mandates that all tax-exempt organizations maintain detailed books and records, primarily to document compliance with tax regulations. Your organization must keep documentation that supports all income, expenses, and credits reported on your annual returns; see the IRS recordkeeping requirements for exempt organizations. These records must remain available for IRS inspection even if you file Form 990-N or aren’t required to file a return at all, per the same IRS guidance. Nebraska law also establishes specific record retention requirements under statute § 21-19,165.

Changes to board or bylaws

Whenever you modify your nonprofit’s bylaws, you must follow specific procedures. Amendments typically require approval by your board of directors or members, depending on your organizational structure; see Nebraska statute 21-19,114. Bylaws affecting director numbers, board composition, terms of office, or selection methods often need member approval; see statute 21-19,114.

When these types of changes require updates to organizational documents filed with the state, Labyrinth can coordinate the necessary update filings to keep your records current with the Secretary of State.

Local permits or licenses for fundraising

Critically, Nebraska has no statewide charitable solicitation registration requirement; see the Nebraska information for charitable solicitors. Yet, this doesn’t mean fundraising is unregulated. Some local governments may require permits or registrations for fundraising activities within their jurisdictions.

You should research the requirements in each community where you plan to solicit donations. Cities and counties may have their own ordinances governing charitable fundraising, and professional fundraising consultants or solicitors may need separate registration.

Frequently Asked Questions