At a Glance

New York nonprofits must complete several annual filings to maintain good standing, including federal Form 990 submissions and state CHAR500 reports to the Attorney General’s Charities Bureau. Form 990 is due by the 15th day of the fifth month after your fiscal year ends (May 15 for calendar-year organizations), while CHAR500 deadlines vary by registration type but generally follow similar timing. Missing these deadlines can result in penalties, loss of tax-exempt status, or registration revocation.

Introduction

Fortunately, staying compliant isn’t impossible when you understand exactly what’s required. Your nonprofit must juggle federal tax filings like the Form 990, state-specific submissions such as the CHAR500, and various tax exemption renewals to remain in good standing.

This step-by-step guide breaks down everything you need to know about maintaining your New York nonprofit’s compliance. We’ll walk you through each essential filing, deadline, and requirement so you can focus on what really matters – your mission and impact. Let’s get your nonprofit’s paperwork in perfect order!

Step 1: File Your IRS Form 990

Filing your IRS Form 990 is the cornerstone of maintaining your nonprofit’s tax-exempt status. This federal requirement applies to almost all tax-exempt organizations and serves as a public disclosure of your financial activities.

Determine which version of Form 990 to file

• Form 990-N (e-Postcard): For organizations with gross receipts normally ≤ $50,000 (see IRS guidance on which Form 990 to file).
• Form 990-EZ: For organizations with gross receipts < $200,000 and total assets < $500,000 (see IRS guidance on which Form 990 to file).
• Form 990: For organizations with gross receipts ≥ $200,000 or total assets ≥ $500,000 (see IRS guidance on which Form 990 to file).
• Form 990-PF: Required for all private foundations, regardless of financial status (see IRS guidance on which Form 990 to file).

Additionally, if your nonprofit has unrelated business income of $1,000 or more, you must file Form 990-T alongside your regular Form 990 submission (see the IRS overview of Form 990-T).

Understand the filing deadlines and extensions

Your Form 990 is due on the 15th day of the fifth month after your fiscal year ends (see IRS annual return deadlines). For organizations following a calendar year (January–December), this means May 15. If your fiscal year ends on June 30, your deadline would be November 15.

Need more time? You can request an automatic six-month extension by filing Form 8868 before your original deadline (see IRS extension information). Remember, although the extension gives you more time to file, it doesn’t extend any payment deadlines if you owe taxes.

Avoid penalties and revocation of tax-exempt status

Failing to file on time carries significant consequences. The IRS imposes daily monetary penalties that increase with an organization’s size and can be substantial; consult IRS Form 990 resources and tools for current amounts and thresholds.

Furthermore, if your organization fails to file for three consecutive years, the IRS will automatically revoke your tax-exempt status (see IRS automatic revocation guidance). This revocation becomes effective on the original filing due date of the third missed annual return. Reinstatement requires filing a new application for tax-exempt status (Form 1023 or 1024) with appropriate fees (see IRS reinstatement procedures).

• Your organization loses tax exemption and may need to pay federal income taxes
• Donors can no longer claim tax deductions for their contributions
• You’ll be removed from the IRS Publication 78 list of tax-exempt organizations
• Reinstatement requires filing a new application for tax-exempt status (Form 1023 or 1024) with appropriate fees

To safeguard your nonprofit’s standing, set calendar reminders for filing deadlines, assign specific responsibility for compliance, and consider working with a tax professional who specializes in nonprofit organizations. Many nonprofits find that partnering with compliance specialists helps ensure accurate, timely submissions while allowing leadership to focus on mission-critical activities. Labyrinth, Inc. helps nonprofits prepare and submit these required annual filings, tracking deadlines and organizing documentation to maintain good standing with federal agencies.

Step 2: Submit the CHAR500 to the NY Charities Bureau

After handling your federal IRS requirements, your New York nonprofit must comply with state regulations by filing the CHAR500 annual report with the NY Charities Bureau. This critical state filing maintains your organization’s good standing with New York authorities.

Who must file the CHAR500

Almost all charitable organizations operating in New York State must register and file annual financial reports with the Office of the New York State Attorney General’s Charities Bureau (212-416-8401, ag.ny.gov). See the Charities Bureau CHAR500 filing guidance for details.

• Conduct charitable activities in New York
• Hold property for charitable purposes in New York
• Solicit charitable contributions (including foundation and government grants) in New York

While most organizations must register, certain exceptions exist. Religious organizations are specifically exempt from registration requirements. If you believe your organization qualifies for an exemption, you can claim it during the online registration process (see the Charities Bureau guidance on registration and exemptions).

Moreover, community funds collected for an individual who is ill or suffered a tragedy are not considered charities and remain exempt from registration, provided all contributions go directly to the intended beneficiary (see the Charities Bureau’s CHAR500 guidance).

Required attachments and audit thresholds

Your CHAR500 filing must include several supporting documents:

• A copy of your IRS Form 990, 990-EZ, or 990-PF with all schedules
• Financial statements based on your revenue thresholds as required by the Charities Bureau (see the CHAR500 instructions)

Annual CHAR500 filings are submitted electronically through the Charities Bureau’s online system. The system accepts supporting documents in PDF and requires two electronic signatures—typically one from your president or authorized officer and another from someone with fiscal responsibility such as your CFO or treasurer (see the CHAR500 e-file guidance).

Filing deadlines and late penalties

The CHAR500 filing deadline varies depending on your registration type (see New York filing deadlines for CHAR500):

• For organizations registered under Article 7-A or dual registrants: Due by the 15th day of the 5th month after your fiscal year ends
• For EPTL-only registrants: Due by the last day of the 6th month after your fiscal year ends

For instance, if your fiscal year ends December 31, your deadline would typically be May 15 (for Article 7-A or dual registrants) or June 30 (for EPTL-only registrants).

Fortunately, the Charities Bureau grants an automatic 180-day extension without requiring a written request (see New York automatic extension notice). This gives you additional time to prepare your filing without penalty.

Failing to file on time can result in serious consequences. For Article 7-A registrants, your registration may be automatically revoked, and you could face civil penalties of $1,000 per violation plus up to $100 per day for continued non-compliance. EPTL registrants may incur fines of $10 per day up to a maximum of $1,000 for each failure. Organizations registered under both Article 7-A and EPTL (dual registrants) face penalties under both laws if they fail to comply with filing requirements (see the Charities Bureau penalty schedule). We help track these varying deadlines and prepare accurate filings to avoid such penalties, especially for organizations operating across multiple states with different renewal schedules.

Step 3: Renew State Tax Exemptions (If Applicable)

Maintaining various tax exemptions is a crucial component of your New York nonprofit’s annual compliance strategy. Beyond federal and charitable registration requirements, your organization must actively renew several state-level tax exemptions to preserve these valuable benefits.

Corporate franchise tax exemption (Form CT-247)

New York nonprofits must file Form CT-247 to obtain exemption from the state corporation franchise tax. Unlike federal exemptions, receiving your IRS determination letter doesn’t automatically exempt your organization from state taxes (see NY Form CT-247 and instructions). You need to submit this separate application to the New York State Department of Taxation and Finance (518-457-5387, tax.ny.gov).

To qualify for this exemption, your organization must:

• Be organized and operated as a not-for-profit
• Not have stock, shares, or certificates for stock or shares
• Ensure no part of net earnings benefits any officer, director, or member
• Be exempt from federal taxation under IRC section 501(a) (see the CT-247 instructions)

If your organization loses its federal exemption but later has it restored by the IRS, you must file a new Form CT-247 application to reinstate your state exemption (see the CT-247 instructions).

Processing times vary based on volume. Submit your application with copies of your IRS determination letter, articles of incorporation, and bylaws, as directed in the CT‑247 instructions (see the CT-247 instructions).

Sales tax exemption (Form ST-119.2)

To make tax-free purchases in New York, your nonprofit must obtain an Exempt Organization Certificate by filing Form ST-119.2 with the New York State Department of Taxation and Finance. This exemption is not automatic upon receiving your 501(c)(3) status (see Form ST-119.2).

When applying, you must:

• Mark the appropriate box indicating your exempt purpose (religious, charitable, educational, etc.)
• Submit required documentation, including your articles of incorporation
• Provide a copy of your IRS 501(c)(3) determination letter (see Form ST-119.2)

Upon approval, you’ll receive Form ST-119 containing your six-digit NYS sales tax exemption number, along with Form ST-119.1 (Exempt Purchase Certificate) to present when making tax-exempt purchases (see New York sales tax exemption guidance).

Exercise caution when using this exemption. Purchases must be made directly by your organization—not by individuals using personal funds even if they’ll be reimbursed later. Misuse of your exempt certificate can result in significant penalties under state law (see New York sales tax exemption guidance).

Real property tax exemption renewals

For nonprofits owning real estate in New York, annual renewal of property tax exemptions is mandatory. Two primary types exist:

Section 420-a (Mandatory): Applies to property owned by nonprofits organized exclusively for religious, charitable, educational, hospital, or moral/mental improvement purposes (see NY property tax exemption renewals).

Section 420-b (Permissive): Covers property owned by organizations for bible, tract, benevolent, scientific, literary purposes, among others. Local tax authorities have discretion to grant these exemptions (see NY property tax exemption renewals).

To renew these exemptions, file form RP-420-a/b-Rnw-I (organization purpose) and RP-420-a/b-Rnw-II (property use) before the taxable status date—often March 1 in many communities. One copy must be filed in each assessing unit where you seek exemption renewal (see renewal instructions and deadlines).

Questions about how late renewals affect existing exemptions can involve legal and factual determinations; consult your assessor or counsel for guidance. Also note that certain special district charges (e.g., for fire, water, or sewer services) may still apply even when a property tax exemption is granted. Check with your local assessor (see NY property tax guidance).

Step 4: Maintain Fundraising Compliance

Fundraising compliance represents a critical aspect of your New York nonprofit’s annual filing obligations. Beyond tax filings, you must maintain proper registration to solicit contributions legally in New York State.

Renew charitable solicitation registration

Your charitable solicitation registration must be renewed annually by filing the CHAR500 form. This renewal is due by the 15th day of the fifth month after your fiscal year ends for Article 7-A or dual registrants, giving organizations with a December 31 fiscal year end a May 15 deadline (see CHAR500 renewal guidance). The Charities Bureau automatically extends this deadline by six months without requiring a written request (see automatic extension notice).

When renewing, you must include your IRS Form 990, 990-EZ, or 990-PF, along with all required schedules. Organizations must also include the level of financial statements required based on their revenue in accordance with Charities Bureau rules (e.g., independent CPA review or audit when applicable) (see Charities Bureau financial statement requirements). We help organizations operating across multiple states coordinate these various charitable registration renewals and track deadlines to maintain good standing in all jurisdictions.

Understand dual registration under Article 7-A and EPTL

• Article 7-A: Applies to organizations soliciting contributions in New York (from residents, foundations, corporations, or government agencies) (see NY Article 7-A and EPTL instructions).
• EPTL: Required for charitable organizations incorporated in or conducting activities within New York State (see NY Article 7-A and EPTL instructions).

Based on these requirements, your nonprofit will fall under one of three registration categories (see the Charities Bureau’s CHAR500 page):

• Article 7-A only (soliciting contributions but not incorporated/operating in NY)
• EPTL only (incorporated/operating in NY but not soliciting contributions)
• Dual registration (both soliciting contributions and incorporated/operating in NY)

Dual registrants need only file one set of annual financial documents, though fees from both Article 7-A and EPTL must be paid. The EPTL fee structure is based on your organization’s net worth, ranging from $25 for organizations with less than $50,000 to $1,500 for those exceeding $50,000,000.

Disclose professional fundraiser contracts

Anytime your nonprofit contracts with professional fundraisers, fundraising counsels, or commercial co-venturers, you must disclose these relationships. These contracts must be in writing and filed with the Charities Bureau in accordance with New York Executive Law (generally within 10 days of execution or before solicitation begins) (see Charities Bureau fundraising professional requirements).

• Clear description of services
• Financial terms
• Statement of the charity’s cancelation rights
• Dated signatures of all parties

Additionally, you must complete Schedule 4a of your CHAR500 filing if you employed professional fundraisers. For longer campaigns, the professional fundraiser may be required to file interim or closing statements as set out in New York Executive Law (see Charities Bureau fundraising guidance).

First and foremost, verify that any fundraising professional you engage is properly registered with the New York State Attorney General’s Charities Bureau to avoid potential penalties (see Charities Bureau fundraising guidance).

Step 5: Meet Governance and Reporting Obligations

Beyond external filings, proper nonprofit governance requires internal documentation and reporting. These practices ensure your organization maintains transparency and legal compliance.

Hold annual board meetings and elections

New York law mandates that nonprofits keep complete and accurate minutes of all board, member, and executive committee meetings. The law also provides rules for the use of electronic meetings and written consents; consult the Attorney General’s governance guidance and the guidance on electronic meetings as well as your bylaws for details.

File conflict of interest disclosures

New York not-for-profit corporations must adopt a conflict of interest policy as required by law. Directors should complete disclosure statements when they join and on a regular basis, consistent with your policy and applicable statute (see the Attorney General’s governance guidance).

Prepare and distribute annual financial reports

Every nonprofit must file annual financial reports with proper documentation. Subsequently, these reports require two signatures—your president or authorized officer plus your CFO, treasurer, or someone with fiscal responsibility (see the Charities Bureau CHAR500 requirements). Consequently, maintaining accurate financial records is essential, as these documents become publicly available. Primarily, these disclosures help donors assess your organization’s fiscal health.

Conclusion

Maintaining your New York nonprofit’s annual filing requirements might seem overwhelming at first glance. However, breaking down these requirements into manageable steps makes nonprofit compliance achievable. Your organization must stay current with both federal obligations like Form 990 and state requirements such as the CHAR500, while also managing tax exemptions and fundraising regulations.

Timely submissions protect your tax-exempt status and help you avoid costly penalties. Missing deadlines for three consecutive years could result in automatic revocation of your federal tax-exempt status, while state-level non-compliance may trigger fines and potential registration cancelation.

Remember that compliance extends beyond paperwork. Board governance, conflict of interest disclosures, and proper financial reporting all play crucial roles in maintaining your nonprofit’s good standing. These elements work together to ensure transparency and accountability to donors, regulators, and the public you serve.

Consider creating a compliance calendar that marks all critical deadlines throughout your fiscal year. This approach will help you plan accordingly and avoid last-minute scrambles to gather necessary documentation. Additionally, assigning specific compliance responsibilities to board members or staff ensures accountability and prevents important filings from slipping through the cracks. Many organizations find that working with dedicated compliance specialists provides reliable support for managing these complex requirements while allowing leadership to focus on mission-driven activities. Labyrinth helps organize filing details, manages deadline reminders, and coordinates agency correspondence to support nonprofits throughout the annual filing process.

Your nonprofit’s mission deserves your full attention. Therefore, establishing efficient systems for managing these administrative requirements frees you to focus on your core purpose rather than paperwork. Though challenging at times, proper compliance protects the valuable work your organization does every day for New Yorkers who depend on your services.

Frequently Asked Questions