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Did You Pay IRS Penalties During the Pandemic? You Might Be Owed a Refund

The pandemic threw a wrench into just about everything—especially when it came to running a business and managing taxes. Filing deadlines shifted, IRS processing ground to a halt, and taxpayers across Scottsdale, Denver, and Albuquerque found themselves navigating a maze of new rules.

Now, years after the dust has settled, a federal court case is reopening a massive question: Did the IRS improperly charge taxpayers penalties and interest during the COVID-19 pandemic?

If the answer is yes, millions of individuals and small business owners could be owed a refund.

Why This Matters for Your Bottom Line

A recent federal court ruling interpreted disaster relief rules in a way that dramatically expands pandemic-related deadline relief. The issue centers on a specific tax code provision that automatically postpones certain deadlines during federally declared disasters.

Because the COVID-19 federal disaster declaration was active from January 2020 through May 2023, the court concluded that many filing and payment deadlines during that period should have been postponed much longer than the IRS allowed.

For taxpayers, the math is simple: If those deadlines were legally postponed, then the late filing penalties, late payment penalties, and related interest charges assessed during those years were never actually owed.

Close up of a calculator

The Clock is Ticking Toward July 2026

Here is where the urgency kicks in. For many taxpayers, the deadline to protect your right to a refund is July 10, 2026, which ties directly to the statute of limitations for IRS refund claims.

The federal government will likely appeal the court’s decision. However, if you sit back and wait for the legal battle to end, your filing deadline might expire. If that happens, you permanently lose your chance to recover that money—even if the courts eventually side with taxpayers.

What is a Protective Refund Claim?

To prevent the clock from running out, your BackPocket CFO at GeneralCents Accounting recommends filing a protective refund claim. Think of this claim as holding your place in line. It does not guarantee an immediate check, but it preserves your legal right to demand a refund once the courts finalize the broader interpretation of COVID-era relief rules.

Vintage typewriter representing paper documentation

Who Could Get Their Money Back?

The list of potentially affected taxpayers is broad. You might qualify if you fall into any of these categories:

  • Individuals who filed late returns during the pandemic.
  • Business owners hit with late payment penalties.
  • Taxpayers who entered into IRS installment agreements after penalties piled up.
  • Companies or individuals who paid steep IRS interest charges between 2020 and 2023.
  • Anyone whose filing or payment deadline landed within the federal COVID disaster window.

The One Major Frustration

Ironically, reclaiming this money involves a completely outdated process. Current IRS guidance indicates that protective refund claims must be submitted on paper. You cannot e-file this request. You must prepare, print, and physically mail documentation to the IRS to secure your rights.

Let GeneralCents Accounting Review Your Case

Tax law gets messy when emergency relief collides with real-world administration. If your business paid IRS penalties or interest tied to COVID-era delays, John Koloch and our team are here to help.

Whether you operate in Scottsdale, Denver, or Albuquerque, we can review your past returns to determine if filing a protective claim makes sense. Contact GeneralCents Accounting today to schedule a consultation.

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