At a Glance

South Dakota nonprofits must file annual reports with the Secretary of State by the first day of their anniversary month for $10 (or $25 for paper filing), plus submit federal Form 990 to the IRS by the 15th day of the fifth month after their fiscal year ends. Most organizations do not need charitable registration unless they use paid telephone solicitors, and eligible nonprofits should renew their sales tax exemption every five years.

Introduction

Running a nonprofit in South Dakota comes with important responsibilities that extend beyond your mission work. Each year, you need to submit specific documents to both federal and state authorities to maintain your good standing. However, keeping track of these requirements can feel overwhelming when you’re focused on serving your community.

Thankfully, staying compliant doesn’t have to be complicated. With a clear understanding of the necessary steps, you can make nonprofit compliance manageable while avoiding potential penalties and fees. This step-by-step guide will walk you through everything you need to know about maintaining your existing South Dakota nonprofit—from IRS Form 990 submissions to state annual reports and beyond. Let’s ensure your organization remains in perfect standing so you can continue focusing on what matters most: your mission!

Step 1: File IRS Form 990

Filing your annual federal tax forms is the cornerstone of maintaining your nonprofit’s tax-exempt status. The IRS requires most nonprofits to submit Form 990 each year, which provides transparency about your organization’s activities, governance, and finances.

Determine which version to file: 990, 990-EZ, 990-N, or 990-PF

Your organization’s size and classification determine which version of Form 990 you’ll need to file. The IRS establishes clear thresholds based on your annual gross receipts and total assets:

• Form 990-N (e-Postcard): For small organizations with gross receipts normally $50,000 or less. This simple electronic filing requires basic information about your nonprofit.
• Form 990-EZ: For organizations with gross receipts less than $200,000 and total assets less than $500,000. This shortened version is less complex than the full Form 990.
• Form 990 (Long Form): Required for larger organizations with gross receipts of $200,000 or more or total assets of $500,000 or more. This comprehensive form includes detailed questions about your financial environment, governance, and operations.
• Form 990-PF: Specifically for private foundations, regardless of financial status or size. This specialized form includes additional questions about a foundation’s assets and financial activities.

Additionally, if your organization has unrelated business income of $1,000 or more, you’ll need to file Form 990-T alongside your regular form.

Understand the due date: 15th day of the 5th month after fiscal year end

Your Form 990 submission deadline depends on when your fiscal year ends. The standard due date is the 15th day of the fifth month after your accounting period closes. For instance, if your fiscal year ends December 31, your form is due May 15 of the following year.

If your deadline falls on a Saturday, Sunday, or legal holiday, it automatically extends to the next business day.

Need more time? You can request an automatic six-month extension by filing Form 8868 before your original deadline. However, the 990-N due date cannot be extended, though there is no penalty for late filing unless it’s the third consecutive missed year.

Use an IRS-approved e-file provider

Since July 2019, the IRS mandates electronic filing for all 990 series forms.

To file electronically, use an IRS list of authorized e-file providers. The IRS also publishes a current roster of MEF providers for Form 990/990‑EZ.

When selecting a provider, verify that their software includes all schedules and attachments your organization needs.

Failing to file your required Form 990 for three consecutive years will result in automatic revocation of your tax-exempt status; see the South Dakota Division of Consumer Protection guidance for charities.

Step 2: Submit the South Dakota Annual Report

Beyond federal tax filings, all South Dakota nonprofits must submit an annual report to the Secretary of State. This critical filing keeps your organization in good standing and ensures the state has current information about your nonprofit. For organizations managing annual filing requirements across multiple states, we help track deadlines and coordinate submissions to ensure all renewal requirements are met consistently.

Find your anniversary month

The timing of your annual report depends on when you initially formed your nonprofit. Unlike some states that use a standard calendar date, South Dakota ties each organization’s filing deadline to its birthday. Your report is due on the first day of your anniversary month each year, as outlined by the South Dakota Secretary of State. For example, if you incorporated on July 20, your annual report would be due every July 1 thereafter.

Not sure when your organization was formed? You can verify your anniversary month using the Secretary of State’s business search tool. The database will display your next annual report due date.

You can submit your annual report starting two months before the due date.

Choose online or paper filing

1. Online Filing: The most efficient and cost-effective option. Visit the Secretary of State’s online filing portal, enter your Business ID number, and follow the prompts.
2. Paper Filing: Download the appropriate form from the Secretary of State’s business forms page. Choose the specific form for domestic or foreign nonprofit corporations based on where your organization was initially formed.

Paper submissions generally require more time to process. Online filings receive immediate confirmation, while paper forms may take longer.

Include required business and officer information

When preparing your annual report, you’ll need to provide or verify:

• Your nonprofit’s exact legal name and South Dakota Business ID number
• Principal office address (physical street address)
• Mailing address (if different from principal address)
• Registered agent information, including physical address in South Dakota
• Names and addresses of your principal officers and directors (see the Secretary of State’s Annual Report instructions)

For domestic nonprofits (formed in South Dakota), anyone with authority may file the report, and original signatures are not required. Foreign nonprofits (formed outside South Dakota) follow similar requirements but use a different form.

Pay the $10 online or $25 paper fee

The standard filing fee for nonprofit annual reports is $10. Effective July 1, 2016, the state implemented an additional $15 processing fee for paper submissions, so mailing your annual report costs $25 in total. Online payments may be made using Visa, MasterCard, Discover, or American Express. See the Secretary of State’s Annual Report instructions and general filing information for details.

Be aware that missing your deadline can result in penalties. Late annual reports incur a $50 late fee, and prolonged non-compliance may lead to administrative dissolution of your nonprofit.

Step 3: Renew Charitable Registration (if applicable)

Unlike many states, charitable registration requirements in South Dakota follow a unique approach for nonprofits seeking to maintain compliance. Understanding whether these rules apply to your organization is essential for avoiding potential penalties and maintaining proper standing.

Check if your nonprofit uses paid solicitors

South Dakota does not have licensing or registration requirements for most nonprofit or charitable organizations; see the state’s charity guidance from the Division of Consumer Protection. Direct mail solicitations by charities do not require registration in the state.

Your nonprofit likely falls into this exempt category if you:

• Operate as a traditional nonprofit organization
• Solicit donations directly through your own staff or volunteers
• Conduct fundraising campaigns via direct mail
• Do not employ external paid solicitors for telephone campaigns

The primary exception involves paid solicitors—third-party professionals hired to conduct telephone solicitation campaigns on behalf of charitable organizations. These individuals must register and maintain bonding with the Attorney General’s Office, Division of Consumer Protection.

Some local jurisdictions may have their own rules for in-person solicitation at the local level.

Submit renewal to the Attorney General’s office

For organizations utilizing paid solicitors, registration follows timelines established by state law. Each paid solicitor must register with the South Dakota Attorney General’s Office, Division of Consumer Protection, before conducting any solicitation campaign; see South Dakota Codified Laws, Chapter 37-30.

Registration is time-limited and must be renewed to remain active if the solicitation campaign continues beyond that period. Application forms are prescribed by the Attorney General’s office and must contain all required information.

Include IRS Form 990 and financial statements

Paid solicitors must file a financial report with the Attorney General after completion of a solicitation campaign, and periodic reports may be required for campaigns lasting more than one year. Required information and certifications are outlined in Chapter 37-30 of the South Dakota Codified Laws.

Maintaining accurate records of all filings and communications with regulatory agencies helps ensure compliance and uninterrupted fundraising activities.

Step 4: Maintain Sales Tax Exemption (if eligible)

Securing a sales tax exemption can save your South Dakota nonprofit significant funds, yet maintaining this status requires careful attention to ongoing requirements.

Verify eligibility with the Department of Revenue

Not all nonprofits automatically qualify for sales tax exemption in South Dakota. The state specifically exempts certain nonprofit charitable organizations recognized under 501(c)(3) that devote resources to the relief of the poor, distressed, or underprivileged. Review the South Dakota Department of Revenue’s sales and use tax guidance for eligibility details.

To qualify, your organization should have an actual physical location in South Dakota, be providing services to the community, and hold federal tax-exempt status under 501(c)(3). Obtaining 501(c)(3) status does not automatically exempt your organization from state sales tax; you must apply separately with the Department of Revenue.

Submit Sales Tax Exempt Status Application every 5 years

Relief agencies that qualify must renew their application every five years. See the Department of Revenue’s guidance on exempt entities for renewal information.

Keep your IRS Determination Letter on file

Your IRS determination letter serves as crucial documentation for maintaining your sales tax exemption. Store both physical and electronic copies of this document securely.

When making tax-exempt purchases, three conditions must be met: presentation of an exemption certificate by an authorized official, payment from the entity’s own funds, and retention of title in the organization’s name. Personal purchases by staff or members are not exempt; see the Department of Revenue’s Exempt Entities guidance (PDF). The Department recommends that businesses review exemption certificates annually.

Step 5: Keep a Registered Agent in South Dakota

Maintaining a registered agent represents another vital requirement for your nonprofit’s ongoing compliance in South Dakota. This designated representative serves as your organization’s official point of contact for legal documents.

Ensure your agent has a physical address in the state

South Dakota law requires your registered agent to maintain an actual street address within the state—P.O. boxes or virtual addresses do not fulfill this requirement. The agent must be available during normal business hours to receive important documents. Your agent may be an individual resident, a domestic organization, or a foreign entity authorized to provide registered agent services.

Update agent info using the Statement of Change form

Any time your registered agent information changes, you must file a Statement of Change with the South Dakota Secretary of State. You can complete the filing online for $10 via the Secretary of State’s Business Services portal, or by mail with an additional $15 paper processing fee using the Statement of Change instructions and the Statement of Change form (PDF).

Be prepared to provide your organization’s name, business ID number, and complete information about your new registered agent.

Consider using a commercial registered agent for privacy

Using a commercial registered agent instead of listing yourself can help keep personal information off public records and avoid receiving legal notices in front of staff or clients.

Frequently Asked Questions

Conclusion

Maintaining your South Dakota nonprofit’s compliance requires diligent attention to several key filing requirements. Throughout this guide, you’ve learned about the essential steps needed to keep your organization in good standing with both federal and state authorities.

Regular submission of your IRS Form 990 stands as the foundation of preserving tax-exempt status, while timely filing of your South Dakota Annual Report ensures state-level compliance. Additionally, organizations working with paid solicitors must address charitable registration requirements, though South Dakota offers more flexibility than many other states.

Eligible nonprofits should renew their sales tax exemption every five years, maximizing available resources for mission-focused work rather than unnecessary tax expenses. Finally, maintaining a qualified registered agent provides crucial protection for your organization when receiving important legal documents.

Missing deadlines can result in substantial penalties, including late fees, loss of good standing, or eventually, revocation of your tax-exempt status. For nonprofits operating across multiple states, working with compliance specialists can help track deadlines, coordinate filings, and ensure all requirements are met consistently.

By managing these compliance requirements effectively—from annual state filings to federal tax submissions—you can protect your organization’s standing and continue focusing your energy where it matters most: serving your community and fulfilling your mission.