Welcome to the IRS weekly roundup for the last week of September 2026. It was one of the busiest tax weeks of the year. The IRS revoked decades of outdated guidance. It also published its full 12-month agenda, updated travel deduction rates, clarified retirement plan deadlines, and raised estate tax fees. Here is every major update, explained in plain language.

1. IRS Revokes 71 Outdated Tax Guidance Documents (Sept 29, 2026)

On September 29, 2026, the IRS revoked 71 pieces of tax guidance in a single move, issuing Notice 2026-58. The revoked revenue rulings, revenue procedures, notices, and other documents “no longer provide useful information,” according to the agency.

Why it happened: In fact, the move is part of a broader federal deregulation push. The IRS says removing dead guidance will streamline tax administration, reduce the volume of rules taxpayers and advisers must review, and increase clarity of the tax law.

What was revoked: The documents range from a 1954 revenue ruling on municipal bonds to 2023 and 2024 rulings. For example, the 2023 and 2024 rulings covered transition periods for the minimum reporting threshold on third-party network transactions (platforms like eBay). They became obsolete after the 2025 tax law repealed the underlying tax code section.

What it means for you: If you or your adviser were still referencing any of these older rulings, they no longer apply. However, this is a cleanup, not a tax increase. It signals that the IRS is actively rewriting the rulebook.

2. IRS Releases 2026-2027 Priority Guidance Plan: 121 Projects (Sept 2026)

The Treasury Department and IRS released the 2026-2027 Priority Guidance Plan. It identifies 121 guidance projects that will get priority resources from October 1, 2026 through September 30, 2027. Starting with this plan, the annual guidance cycle now matches the federal fiscal year.

Key focus areas:

Continued implementation of the One, Big, Beautiful Bill Act (OBBBA)

Deregulation and burden reduction across the tax code

Tax-exempt organizations and nonprofit rules

Tribal tax issues and digital assets

Clean fuel production credit, research and experimental expenditures, the qualified business income (QBI) deduction, and international tax provisions

What it means for you: The 2025 tax law is still being implemented. As a result, expect a steady stream of new regulations over the next 12 months affecting deductions, credits, and reporting.

3. New IRS Per Diem Rates Effective October 1, 2026

The IRS announced special per diem rates for travel away from home on or after October 1, 2026, under IRS Notice 2026-60 (issued September 25, 2026).

Employers using these rates can treat certain travel expenses as substantiated without employees proving actual amounts spent

Employees must still substantiate the time, place, and business purpose of travel

The notice replaces IRS Notice 2025-54 and covers the high-low substantiation method, special rates for transportation industry employers, and incidental-expenses-only rates

General per diem guidance issued in 2019 (post Tax Cuts and Jobs Act) remains in effect

What it means for you: Therefore, if your business pays per diem allowances, update your rates and policies for travel on or after October 1, 2026.

4. IRS Clarifies SECURE and SECURE 2.0 Retirement Plan Amendment Deadlines (Sept 18, 2026)

The IRS issued new guidance on SECURE Act and SECURE 2.0 amendment deadlines. The key question was whether plans must follow the Notice 2024-2 deadlines (generally December 31, 2026) or the deadlines on an applicable Required Amendments List. The answer depends on whether the amendment is required or discretionary.

Required amendments: The deadline is generally the end of the remedial amendment period, the last day of the second calendar year following the year the amendment is adopted or effective

For example, the IRS expects the SECURE 2.0 Roth catch-up requirement on the 2027 Required Amendments List. This sets the amendment deadline at generally December 31, 2029.

In addition, the IRS expects automatic enrollment requirements, long-term part-time employee rules, and required minimum distribution provisions on future RA Lists once it issues final regulations.

What it means for you: If your business sponsors a 401(k) or other retirement plan, confirm with your plan administrator which amendments are required versus discretionary and calendar the correct deadlines.

5. IRS Issues New Guidance Targeting ETF Tax Transactions (Sept 29, 2026)

Meanwhile, on September 29, 2026, the IRS released Revenue Ruling 2026-20 and Notice 2026-62, tightening tax enforcement around ETF in-kind transactions.

The IRS now prohibits contributions where investors exchange appreciated portfolios for ETF shares with a different investment thesis

Notice 2026-62 targets selective swap terminations and other in-kind distributions designed to avoid nonqualifying income

The public comment deadline is October 28, 2026

What it means for you: Funds may change their in-kind contribution policies to comply, which could affect the tax efficiency of certain ETF portfolios. Investors should review holdings with their advisers.

6. Estate Tax Closing Letter Fee Increases to $76 (Effective Oct 26, 2026)

Treasury and the IRS finalized regulations (T.D. 10055, September 25, 2026) increasing the user fee for requesting an IRS estate tax closing letter (Letter 627) from $56 to $76 for requests received on or after October 26, 2026. The final rules adopt the June 2026 proposed regulations without substantive change.

What it means for you: Executors and estate attorneys should file closing letter requests before October 26, 2026 to pay the lower $56 fee.

7. New Guidance Coming for Nonprofits and Tax-Exempt Organizations

The Priority Guidance Plan includes several projects affecting tax-exempt organizations, as detailed by KPMG:

OBBBA implementation: Regulations under Section 4960 on excess compensation paid by tax-exempt organizations, including the expanded definition of covered employee

Excise tax rules under Section 4968 on investment income of certain private colleges and universities (OBBBA implementation)

A new income tax credit under Section 25F for contributions to scholarship granting organizations (OBBBA implementation)

Deregulation: Rules under Section 4945 on expenditure responsibility and Section 6104 on public inspection of exempt organization materials

On September 4, 2026, the IRS published proposed regulations on applying the fundamental public policy against racial discrimination in determining private school eligibility for 501(c)(3) status.

What it means for you: Consequently, nonprofits face some of the heaviest upcoming changes. Executive compensation, investment income taxes, and 501(c)(3) eligibility rules are all in motion.

8. Tax Court and State Highlights

A weekly federal and state roundup also flagged these developments for the week ending September 27, 2026:

Tax Court (precedential BBA partnership decision): The 90-day petition deadline under Section 6234(a) is subject to equitable tolling, applied after IRS misinformation caused a late petition

IRS released procedural guidance on automatic accounting method changes for research expenditures

Proposed regulations on CFC pro rata share allocations and on nondiscrimination mandates for tax-exempt schools

Ohio Supreme Court ruled the Commercial Activity Tax reaches only amounts actually received after distributor chargebacks, not list prices (Perrigo Sales Corp.)

Indiana Tax Court affirmed a major industrial property valuation dispute

What it means for you: Partnerships under audit get a fairer shot at Tax Court review. Moreover, multistate businesses should watch the Ohio CAT ruling for gross receipts calculations.

What Should Your Business Do After This IRS Weekly Roundup?

Confirm no one on your team still relies on the 71 revoked rulings

Update travel per diem policies for the October 1, 2026 rates

Review retirement plan amendment deadlines with your plan administrator

If you hold ETFs, review in-kind transaction exposure before the October 28 comment deadline

Nonprofits: track the 4960, 4968, and 501(c)(3) rulemakings closely

If this IRS weekly roundup feels like a lot to track alone, that is exactly what we do for our clients every week.

How Funds to Function Can Help

Weekly IRS updates like these are difficult to follow while running a business. Funds to Function helps US businesses and nonprofits stay compliant with practical, ongoing support:

Compliance monitoring: we track new IRS guidance, deadlines, and regulatory changes that affect your business, so nothing is missed

Bookkeeping and payroll: accurate, up-to-date books that keep you ready for every filing deadline

Tax planning: plain-language guidance on how new rules affect your deductions, credits, and reporting

Nonprofit and 501(c)(3) services: support with exemption requirements, executive compensation rules, and Form 990 readiness as regulations evolve

Retirement plans: we coordinate with your plan administrator to keep SECURE 2.0 amendment deadlines on track

To discuss what these updates mean for your business, book a free 15-minute consultation: calendly.com/fundstofunction-info/15min

Disclaimer

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