At a Glance

Iowa nonprofits must file biennial reports (every two years) with the Secretary of State during odd-numbered years between January 1st and April 1st, plus annual federal Form 990 filings with the IRS. Most nonprofits also pay sales tax on purchases unless specific exemptions apply.

Introduction

Staying on top of nonprofit annual filing requirements is crucial for your Iowa organization’s survival. Missing deadlines can result in hefty penalties, loss of tax-exempt status, and even involuntary dissolution of your nonprofit corporation.

Fortunately, maintaining compliance doesn’t have to be overwhelming. With proper planning and knowledge, you can navigate Iowa’s regulatory landscape with confidence. This step-by-step guide will walk you through everything you need to know about your ongoing filing obligations—from Iowa’s biennial report requirements to federal Form 990 submissions and sales tax considerations.

Whether you’re managing a small community organization or a large charitable foundation, understanding these requirements will help you protect your nonprofit’s standing and focus on what truly matters: your mission. Let’s dive into the essential filings that keep your nonprofit legally compliant and ready to serve your community.

Understanding Iowa’s Biennial Report Requirement

Iowa nonprofits must maintain good standing with the Secretary of State through regular reporting. Unlike many states that require annual filings, Iowa operates on a biennial schedule for nonprofit corporations. This means your organization needs to file reports every two years rather than annually.

What the biennial report includes

The biennial report for Iowa nonprofits serves as an update to your organization’s essential information. When preparing your report, you’ll need to include:

• Current name and address of your registered office
• Name and address of your registered agent who accepts legal documents
• Names and addresses of your current officers and directors
• Brief description of your nonprofit’s activities
• Federal Employer Identification Number (FEIN)
• Signature of an authorized officer (typically president or secretary)

This report helps the state maintain accurate records about your organization. Additionally, it provides transparency to the public about who runs your nonprofit and how to contact your organization officially.

When and how to file

Iowa requires nonprofits to file their biennial reports during odd-numbered years. The reporting period begins on January 1st and continues through April 1st of these odd-numbered years. For example, if your nonprofit was incorporated in 2022, your first biennial report would be due during the January–April filing period of 2023.

1. Online Filing: The most efficient method is through the Iowa Secretary of State Business Entities Online portal (515-281-5204). Online filing provides immediate confirmation and reduces the chance of errors.
2. Mail Submission: If you prefer paper filing, you can download the form from the Secretary of State website, complete it, and mail it with the appropriate fee.
3. In-Person Delivery: You may also deliver your completed form to the Secretary of State’s office in Des Moines.

A filing fee applies to nonprofit biennial reports; verify the current amount on the Secretary of State’s website before filing. We can streamline this process by preparing and filing biennial reports on your behalf, ensuring accuracy and timely submission while tracking all renewal deadlines through our comprehensive filing management system.

What happens if you miss the deadline

Missing your biennial report deadline can have serious consequences for your nonprofit. If you fail to file by April 1st of the reporting year, your organization enters “delinquent” status. During this period, you can still file the report; Iowa may assess a late fee in addition to the standard filing fee.

However, if your nonprofit remains delinquent for an extended period after the filing deadline, the Secretary of State may administratively dissolve your corporation. Once dissolved, your organization loses its legal standing as a corporation in Iowa, which can have far-reaching implications:

• You may lose liability protection for board members and officers
• Your organization can no longer legally operate under its name
• Your bank accounts may be frozen
• Your tax-exempt status could be jeopardized

Fortunately, you can apply for reinstatement if your nonprofit is administratively dissolved. This process requires filing for reinstatement, paying all outstanding fees and penalties, and submitting any missing biennial reports. Although reinstatement is possible, it’s far simpler to meet your filing deadlines in the first place.

To avoid missing deadlines, set up a compliance calendar with reminders several months before the due date, designate a specific board member or staff person responsible for filing, and consider setting internal deadlines earlier than the actual state deadlines. Labyrinth, Inc. helps organizations maintain tracking systems that organize filing details, deadline reminders, and agency correspondence to prevent these complications.

Federal Annual Filing: IRS Form 990 Series

Beyond state requirements, your Iowa nonprofit has crucial federal filing obligations with the IRS. The Form 990 series serves as the primary tool for the IRS to gather information about tax-exempt organizations, educate organizations about tax law requirements, and promote compliance (see IRS Form 990 resources and tools).

Which Form 990 to file based on revenue

• Form 990-N (e-Postcard): For organizations with gross receipts normally $50,000 or less. This is a simple electronic notice filed online with basic organizational information (see IRS Form 990-N requirements).
• Form 990-EZ: For organizations with gross receipts between $50,000 and $200,000 AND total assets less than $500,000 (see IRS Form 990 filing thresholds).
• Form 990: Required for organizations with gross receipts of $200,000 or more OR total assets of $500,000 or more (see IRS Form 990 filing thresholds).
• Form 990-PF: Required for all private foundations regardless of financial status (see IRS Form 990 filing thresholds).

New organizations have slightly different thresholds. Your nonprofit can file Form 990-N if it has existed for one year or less and received less than $75,000, or existed between one and three years with average gross receipts under $60,000 (see IRS e-Postcard filing requirements).

Key deadlines and extension options

Form 990 is due on the 15th day of the 5th month following the end of your organization’s fiscal year (see IRS due date guidance). For example, if your fiscal year ends December 31st, your filing deadline is May 15th of the following year.

The IRS provides a six-month extension option without requiring you to show cause. To request this extension, submit Form 8868 before your original due date (see IRS annual filing overview). Consequently, if your original due date was May 15th, the extended deadline would be November 15th.

Failing to file on time can result in penalties—$20 per day for each day the return is late, up to $10,500 or 5% of your organization’s gross receipts (whichever is less). Furthermore, if your nonprofit fails to file required Forms 990 for three consecutive years, you will automatically lose your tax-exempt status on the filing due date of the third consecutively missed year (see IRS e-Postcard filing requirements).

What information is made public

Form 990 returns must be made available for public inspection for a three-year period beginning with the due date of the return (including extensions) or the date it’s actually filed, whichever is later (see IRS public disclosure rules). This includes all schedules and attachments filed with the form, except that organizations other than private foundations need not disclose contributor names and addresses.

The public can access your Form 990 through several channels:

1. Online databases: The IRS makes Form 990 data available on its website, specifically through Tax Exempt Organization Search.
2. Third-party websites: Services like Guidestar (now Candid) and ProPublica publish Form 990s (see the Library of Congress guide to Form 990).
3. In-person requests: Your organization must make forms available at your principal office during regular business hours.

Donors, grantors, media, watchdog groups, and other stakeholders often review Form 990s before making decisions about your organization. Therefore, it’s advisable to have your entire board review your Form 990 before filing, both to ensure accuracy and to make sure the form clearly tells your nonprofit’s story.

Sales and Use Tax Responsibilities for Iowa Nonprofits

Unlike income tax exemptions, your nonprofit status generally doesn’t automatically exempt your organization from Iowa’s sales and use tax responsibilities. Understanding these obligations is a critical part of your annual compliance requirements.

When nonprofits must pay sales tax

Contrary to what many assume, nonprofit organizations in Iowa typically must pay sales tax on their purchases (see Iowa Department of Revenue guidance for nonprofit entities). Even with federal 501(c)(3) status and state income tax exemption, your organization remains responsible for sales tax unless another specific exemption applies.

The primary exceptions to this rule include:

• Iowa private nonprofit schools don’t pay sales tax on goods and services used for educational purposes (see Iowa Department of Revenue nonprofit guidance).
• Purchases made specifically for resale are exempt.
• Certain grocery items that are exempt for everyone.

For instance, if your church purchases hymn books, office supplies, or pays for building maintenance, you must pay the standard 6% state sales tax plus any applicable local option sales tax (see Iowa Department of Revenue nonprofit guidance). Meanwhile, a nonprofit animal shelter would pay tax on dog food used at the facility but not on t-shirts purchased for resale as fundraising items.

Purchases for resale vs. direct use

The distinction between items for direct use versus resale significantly impacts your tax obligations. Purchases your nonprofit makes for resale are exempt from sales tax—even if your organization doesn’t have a sales tax permit (see Iowa sales tax guide for nonprofit entities).

Consider these examples:

• When your nonprofit purchases items to use in operations (cleaning supplies, office equipment), these are taxable.
• When you purchase items specifically to resell (fundraising merchandise, auction items), these are exempt from sales tax.

Notably, sales made by educational, religious, or charitable organizations may be exempt when the proceeds are used for qualifying educational, religious, or charitable purposes. Nevertheless, all proceeds from games of skill, chance, raffles, and bingo games are subject to sales tax regardless of who operates them or how proceeds are used—except those operated by a county or city.

Use tax on out-of-state purchases

The Iowa use tax complements sales tax and applies when your nonprofit purchases taxable goods or services from out-of-state vendors who don’t collect Iowa sales tax (see Iowa sales and use tax guide). This tax ensures that purchases made outside Iowa don’t enjoy an unfair advantage over in-state purchases.

The use tax rate matches the state sales tax rate at 6%. If your organization makes taxable out-of-state purchases, you must report and pay use tax accordingly:

• If you owe $1,200 or more in use tax annually, you must register for a sales and use tax permit.
• If you owe less than $1,200 annually, you may report on the Iowa Non-Permit Use Tax Return.

Importantly, if you paid sales tax to another state, Iowa allows a credit. If the other state’s tax rate equals or exceeds Iowa’s 6%, no additional tax is due. Otherwise, you pay only the difference (see Iowa nonprofit entities guidance).

Organizations failing to track and report use tax may face not only the unpaid tax but penalties and interest as well. Consider implementing a regular review of all out-of-state purchases as part of your annual compliance routine.

Consequences of Non-Compliance and How to Fix It

Penalties for late or missed filings

The cost of non-compliance escalates quickly. For late Form 990 filings, the IRS imposes a daily penalty of $20, potentially reaching $10,500 or 5% of your gross receipts (whichever is less). Larger nonprofits face steeper penalties—$105 per day up to an inflation‑adjusted cap (for example, $54,500 for returns required to be filed in 2022) (see IRS penalty guidance for exempt organizations).

Moreover, if your organization misses three consecutive annual filings, the IRS automatically revokes your tax-exempt status. At the state level, failing to file your biennial report can lead to administrative dissolution, causing your nonprofit to cease existing as a separate legal entity.

The IRS may waive penalties if you can demonstrate “reasonable cause” for the late filing. This requires attaching a detailed written statement to your return, made under penalty of perjury, explaining what prevented timely filing and describing the steps taken to prevent future issues.

How to reinstate corporate status

To restore a dissolved Iowa nonprofit, you can use the Secretary of State’s Fast Track Filing system (see Iowa Fast Track Filing help). The process involves:

1. Logging into the Fast Track Filing portal
2. Selecting “Application for Reinstatement”
3. Completing any missed biennial reports
4. Updating registered agent information if necessary
5. Paying all outstanding fees and penalties

Upon approval, your organization’s good standing typically relates back to the dissolution date, as though dissolution never occurred. We help organizations navigate this reinstatement process, handling the paperwork and ensuring all requirements are met for successful restoration.

How to regain tax-exempt status with the IRS

After revocation, you must reapply for tax exemption by filing Form 1023 or 1023-EZ with the appropriate fee (see IRS reinstatement after automatic revocation). The IRS offers several reinstatement paths:

• Streamlined Retroactive Reinstatement: Available to organizations that were eligible to file Form 990-N or 990-EZ and haven’t previously had their status revoked. You must apply within 15 months of revocation (see IRS automatic revocation reinstatement options).
• Retroactive Reinstatement: Requires demonstrating reasonable cause for at least one year’s missed filing, plus submitting all delinquent returns (see IRS automatic revocation reinstatement options).

Afterward, the IRS will include your reinstated organization in its Exempt Organizations database, though you’ll remain on the revocation list as a historical record.

Other Annual Considerations and Special Cases

Unrelated business income and Form 990-T

While your nonprofit enjoys income tax exemptions, any unrelated business income exceeding $1,000 requires filing Form 990-T in addition to your regular Form 990. This applies to income from activities not substantially related to your exempt purpose. Nonprofits must maintain separate books for these activities, as substantial unrelated income—typically exceeding 20% of total income—could jeopardize your tax-exempt status. To clarify, a theater selling concessions during performances relates to its mission, whereas operating a year-round restaurant likely constitutes unrelated business.

Property tax exemption rules

Property tax exemptions aren’t automatic in Iowa. You must apply separately by February 1 to your local assessor (see Iowa property tax exemption application and guidance (PDF)). Once approved, exemptions continue automatically in subsequent years provided the property maintains its qualifying use. Qualification requires the property to be:

• Owned by religious, scientific, or charitable institutions
• Used solely for appropriate nonprofit purposes
• Not exceeding 320 acres
• Not operated for pecuniary profit

Religious institutions can exempt up to 50 acres of grounds.

Do you need to update your registered agent information?

When your organization changes officers, directors, or registered agent information, these updates must be filed with the state. We handle these update filings as part of our corporate filing services, ensuring your nonprofit maintains current information with state agencies and avoiding potential compliance issues.

Fundraising and gambling tax rules

Despite your nonprofit status, gambling activities always incur sales tax in Iowa. This includes raffles, games of chance, and bingo. Before conducting such activities, you must:

• Obtain the appropriate gambling license from the Iowa Department of Inspections & Appeals (515-242-5821) (see Iowa social and charitable gambling licenses).
• Secure a sales tax permit (see Iowa business permit registration).
• Collect sales tax on all gross receipts without deductions (see Iowa sales tax for nonprofit entities).

Whereas non-gambling fundraising may be exempt provided all proceeds support educational, religious, or charitable purposes (see Iowa sales tax FAQ).

Conclusion

Maintaining your Iowa nonprofit’s compliance requires diligent attention to several critical filing obligations. Throughout this guide, you’ve discovered the comprehensive requirements needed to keep your organization in good standing.

First and foremost, remember that Iowa operates on a biennial reporting schedule rather than annual filings. This gives your organization a slight administrative advantage, though missing these less frequent deadlines can still result in administrative dissolution. Therefore, setting up reminders several months in advance becomes essential for timely submissions.

Additionally, your federal compliance hinges on properly filing the appropriate Form 990 variant based on your organization’s size and revenue. The consequences of missing three consecutive filings—automatic revocation of tax-exempt status—can devastate your nonprofit’s operations and reputation.

Sales and use tax considerations often surprise many nonprofit leaders. Your tax-exempt status generally doesn’t exempt you from Iowa’s sales tax obligations unless specific conditions apply. Consequently, understanding when your purchases qualify for exemption versus when they’re taxable remains crucial for proper financial management.

Unrelated business income, property tax exemptions, and fundraising regulations also demand your attention as part of your annual compliance routine. Each area carries its own deadlines, exemption requirements, and potential penalties.

Above all, proactive management of these requirements will save your organization significant stress, money, and reputation damage. Designate specific board members or staff to oversee compliance calendars, create internal deadlines ahead of actual due dates, and consider consulting with a nonprofit attorney or accountant if your situation becomes complex.

Your nonprofit’s mission deserves your full attention and energy. With experienced compliance specialists handling your ongoing filing obligations, you can focus on what truly matters: serving your community. We manage biennial reports, Form 990 filings, and charitable registration renewals to help ensure your organization remains focused on your mission rather than scrambling to fix preventable compliance issues. With proper planning and this guide as your reference, you can confidently navigate Iowa’s nonprofit regulatory requirements and keep your organization thriving for years to come.

Frequently Asked Questions