Nonprofit organizations are vital to our communities, and tax professionals are indispensable advisors to them. Although many nonprofits enjoy tax-exempt status, they still often must file annual information returns with the IRS.

Whether you’re advising these organizations as a tax professional or working within one, staying ahead of due dates and understanding key items is crucial. We will explore the filing deadlines, key items of interest and best practices for working with nonprofit organizations.

Filing deadlines

One of the primary responsibilities of tax professionals working with nonprofits is managing deadlines. Nonprofits have specific filing requirements and due dates that vary based on their year-end.

Form 990 filing deadline:

For most tax-exempt organizations operating on a calendar year, Form 990 is typically due by May 15. Which Form 990 an organization needs to file generally depends on its financial activity. For those on a fiscal year, the deadline falls on the 15th day of the fifth month after the close of the fiscal year. Timely submission is crucial to avoid penalties and maintain tax-exempt status.

Which Form 990 do exempt organizations file?
Status	Form to file
Annual gross receipts normally ≤ 50,000	990-N (e-Postcard) Organizations eligible to file the e-Postcard may choose to file a: 990, Return of Organization Exempt from Income Tax or 990-EZ, Short Form Return of Organization Exempt from Income Tax
Annual gross receipts < $200,000, and total assets < $500,000	990-EZ or 990
Annual gross receipts ≥ $200,000, or total assets ≥ $500,000	990
Private foundation – regardless of financial status	990-PF, Return of Private Foundation

Extensions and exceptions

An extension can be requested if a nonprofit needs more time to file. Form 990, 990-EZ, 990-PF and 990-N are due on the 15th day of the fifth month after the organization’s year-end (May 15 for calendar year organizations). A six-month automatic extension of time can be granted by filing Form 8868, Application for Extension of Time To File an Exempt Organization Return. Form 990-N is not eligible for an extension of time to file.

However, it’s important to note that an extension for filing does not extend the time to pay any taxes due. Tax professionals should ensure clients understand the extension process and its associated implications.

Key items of interest for tax professionals

Beyond deadlines, several specific issues require careful attention when advising nonprofit organizations.

Maintaining tax-exempt status

• IRS compliance requirements: Nonprofits must adhere to strict IRS guidelines. This includes operating exclusively for exempt purposes and avoiding excessive political or lobbying activities. Regularly reviewing organizational activities helps ensure compliance and minimizes the risks of revocation.

• Documentation and record keeping: Thorough documentation of activities, donations and expenditures is essential for compliance and critical in the event of an audit. Tax professionals should advise nonprofits on best practices for maintaining records that support their IRS filings and organizational missions.

Unrelated business income (UBI)

UBI is income from activities unrelated to the organization’s core exempt purpose is subject to taxation. Tax professionals need to work closely with nonprofits to identify any potential UBI, calculate the tax correctly and understand any applicable deductions.

Generally, unrelated business taxable income (UBTI) is gross income from a trade or business, regularly carried on, less the deductions allowed, which are directly connected with the trade or business but not substantially related to the organization’s exempt purpose.

An exempt organization with $1,000 or more of gross income from an unrelated business must file Form 990-T, Exempt Organization Business Income Tax Return (and proxy tax under section 6033(e). If the organization expects its annual tax to be $500 or more, quarterly estimated tax must also be paid. Form 990-W, Estimated Tax on Unrelated Business Taxable Income for Tax-Exempt Organizations, is the worksheet that can be used to calculate the amount of estimated tax payments required. The requirement to file Form 990-T is in addition to the obligation to file the annual information return.

Risk management

Engaging in unrelated business activities can jeopardize a nonprofit’s tax-exempt status if they become a substantial part of its overall operations. Regular assessments and strategic planning can help mitigate these risks.

Donor contributions and fundraising compliance

• Acknowledgment requirements: Nonprofits must provide proper documentation for donations, which is essential for donor tax deductions and compliance. Tax professionals can assist in establishing systems to track contributions accurately and issue timely acknowledgment letters.

• IRS reporting standards: Fundraising activities must be reported accurately on tax forms. Ensuring that all fundraising events are recorded correctly is a critical area of focus.

Best practices for tax professionals

• Develop a comprehensive tax calendar

  Maintain a detailed calendar of all federal, state, and local filing deadlines. This includes Form 990, payroll taxes, UBI filings, and other required filings.

• Conduct regular reviews

  Periodically review the nonprofit’s activities and financial records to ensure ongoing compliance. Internal audits can help identify issues early, preventing potential complications during an IRS audit.

• Educate and communicate

  Ensure that the nonprofit board and staff understand the importance of timely and accurate tax filings. Clear communication can foster a culture of compliance and make it easier to implement necessary changes.

• Invest in training and technology

  Utilize the latest accounting software and invest in regular training to stay current with evolving tax laws and compliance requirements. A well-informed team can prevent costly mistakes and safeguard the organization’s tax-exempt status.

Tax professionals can call the IRS Tax Exempt and Government Entities Customer Account Services at 877-829-5500 (toll-free number) for answers to questions about charities and other non-profit organizations.

For more information on this topic, check out our Preparing Form 990 for Tax Exempt Organizations On-Demand Webinar.

Becoming an enrolled agent (EA) is an excellent way to gain expertise in tax matters and represent taxpayers before the IRS. The process is straightforward and has no education prerequisites, so you can begin immediately. Here’s a step-by-step guide to help you navigate the EA process and earn the highest credential the IRS awards.

Step 1: Obtain a preparer tax identification number (PTIN)

Your PTIN identifies you as a tax professional. Here’s more information you’ll need to know about obtaining a PTIN.

• Eligibility: You must be 18 or older and generally provide your Social Security number (SSN). Foreign people without an SSN can still apply by providing additional documentation.

• How to apply: You can apply online through the IRS website in about 15 minutes. The cost is $19.75.

• Alternative: You can also apply by mailing in Form W-12, IRS Paid Preparer Tax Identification Number (PTIN) Application and Renewal, which will add 4-6 weeks of time.

Step 2: Schedule the IRS Special Enrollment Exam (SEE)

Unless you have been an IRS employee, the IRS requires you to take its Special Enrollment Exam (SEE), a three-part exam covering individual tax, business tax, and IRS practice and procedures.

• How to apply: Book your exams through the Prometric Test Center website. They can be taken in any order.

• Fees and availability: Each exam part costs $267. The test is offered from May 1 to Feb. 28, with a blackout period in March and April.

• Plan accordingly: Be realistic when scheduling your exams, incorporating enough time for studying and planning for life and work events along the way.

Step 3: Achieve passing scores on all three parts of the SEE

The IRS grades on a scale; with 130 being the highest score, you need a minimum of 105 points on each part of the SEE to pass.

• Score validity: Passing scores are valid for up to three years. (After that, you will lose credit and have to retest.) You can also retake each part up to four times per testing period.

• Study tips: Prepare using resources like the National Association of Tax Professionals’ (NATP) EA Exam Review, which offers study materials, practice exams and more.

Step 4: Apply for enrollment

Next, you will apply for official enrollment by submitting Form 23, Application for Enrollment to Practice Before the Internal Revenue Service, to the IRS.

• Application process: You can apply online or by mail (online is faster). The application fee is $140.

• Processing time: After submitting your application, the IRS typically processes it within 60 days. Former IRS employees may face longer processing times.

Step 5: Pass the background check

Finally, the IRS will conduct a background check to ensure you meet tax compliance standards and do not have a criminal record that disqualifies you.

• Disqualifications: Outstanding tax liabilities or criminal offenses involving dishonesty or breach of trust can disqualify you. However, some criminal records can be explained in your application.

Once you pass the background check, congratulations! You will receive your official enrollment card and a wall certificate from the IRS.

Ongoing Requirements for EAs

After becoming an EA, you must maintain your status by completing the following requirements:

• PTIN renewal: Renew your PTIN annually.

• EA renewal: Renew your status every three years, with a $140 renewal fee.

• Continuing education: Complete 72 hours of continuing education over the three-year cycle (at least 16 hours annually), including two ethics credits annually. NATP has a robust library of CPE offerings to help you meet this requirement.

Conclusion

Becoming an EA offers a rewarding career path in taxation. Following these steps and staying committed to education and compliance will make you an elite-status tax professional who can represent clients before the IRS. Best of luck on your journey to becoming an EA!

NATP is here to help

We’re building a free library of guides, blogs and tools to help you become an enrolled agent. Drop your email below, and we’ll send new resources as they’re released. 👇

Navigating IRS transcripts isn’t just about retrieving data – it’s about understanding what that data means and how it can help your clients. In a recent discussion, NATP instructor and tax resolution expert Jim Buttonow shared practical insights on using IRS transcripts more effectively in everyday practice. From recent changes in access to common red flags to watch for, here’s what you need to know.

Understanding IRS transcripts

IRS transcripts are essential tools for reviewing a taxpayer’s filing and payment history. They’re often used to verify returns, track notices, and uncover discrepancies that may lead to compliance issues or refund delays. As a refresher, here are the main types of transcripts:

• Tax return transcript – shows most line items from the original return
  • Available for current and prior three years
• Tax account transcript – includes basic data such as filing status, AGI, taxable income and any payments or adjustments
  • Available for current and prior nine years
• Record of account transcript – combines tax return and tax account transcript data
  • Available for current and prior three years
• Wage and income transcript – contains information from W-2s, 1099s, 1098s and other third-party statements
  • Available for current and prior nine years
• Verification of non-filing letter – confirms that no Form 1040-series return was filed for a given year
  • Available after June 15 for the current tax year and anytime for prior three years

Transcript Type	Description	Availability
Tax return transcript	Shows most line items from the original return	Current year and prior 3 years
Tax account transcript	Includes filing status, AGI, taxable income and any payments or adjustments	Current year and prior 9 years
Record of account transcript	Combines tax return and tax account transcript data	Current year and prior 3 years
Wage and income transcript	Contains W-2s, 1099s, 1098s and other third-party information	Current year and prior 9 years
Verification of non-filing letter	Confirms no Form 1040-series return was filed	After June 15 for current year; anytime for prior 3 years

What’s new for 2025

The IRS continues to modernize transcript tools and access, and this year, several changes are making transcript use easier – and more secure – for tax professionals.

• Redacted data for identity protection – Only partial Social Security numbers and other identifiers are shown, which helps protect taxpayer information.
• Improved online tools – The IRS is enhancing features in its Tax Pro Account and Transcript Delivery System, making it easier to pull the right records quickly.
• More real-time updates – Some data is now updated more frequently, giving you better visibility into the status of returns and notices.

Best practices for transcript use

Transcripts can be a powerful diagnostic tool – if you know how to use them well. Buttonow recommends these tips:

• Review wage and income transcripts early to detect income underreporting issues or overlooked documents
• Use tax account transcripts to help resolve notices related to penalties, payment mismatches or unfiled returns
• Regularly monitor your clients’ transcript data when handling IRS letters or suspected identity theft
• Encourage clients to create their own IRS Online Account for visibility – especially helpful for those dealing with identity theft or refund delays

  Why this matters

Understanding IRS transcripts is essential for proactive tax professionals. They can help you catch filing errors, resolve issues more efficiently and communicate more confidently with the IRS on your client’s behalf. Buttonow shared, “The transcript is often your window into what the IRS sees – and that’s the key to unlocking solutions.”

NATP members stay ahead of changes like these to better serve clients with accuracy, insight and professionalism. If you haven’t explored the latest on IRS transcripts, now’s the time to sharpen your skills.

👉 Watch the conversation with Jim Buttonow below!