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R&D Tax Credits: A Missed Opportunity Hiding in Your Payroll

September 02, 2025

Have you explored the benefits of a Research and Development (R&D) tax credit? Many companies mistakenly believe that just because they don’t wear lab coats, their activities don’t qualify for this valuable credit. This blog explores the benefits of this tax credit, what activities qualify and how you can take advantage.

When Innovation Hides in Your Payroll

Many companies are still unaware that their everyday payroll expenses, especially for technical employees, can qualify for the R&D tax credit. As tax deadlines and funding pressures grow, it’s more important than ever for businesses to explore credits that could improve their cash flow.

If you’re paying employees to test, refine, or develop internal processes or technology, you could be missing out on thousands of dollars in tax credits. Even early-stage businesses and startups with no income tax liability can apply these credits against their payroll taxes. Failing to recognize this is one of the most common, and costly, mistakes we see.

Quick Takeaways

  • R&D tax credits are not just for scientists
  • Payroll wages often make up the largest portion of the credit
  • Startups may apply the credit directly to payroll taxes for up to 5 years
  • Routine process improvements and internal innovation may qualify
  • Many companies miss out due to misconceptions

How Can Payroll Help You Claim the R&D Tax Credit? 

Payroll is often the largest and most overlooked qualifier for the R&D credit. Qualified wages paid to employees who work on technical projects, whether directly or in support, can unlock substantial tax savings.

Which Employees Might Qualify? 

  • Engineers and software developers
  • Team members testing or improving processes
  • Employees involved in technical problem-solving
  • Staff documenting research efforts

These employees don’t need to build new inventions. If they’re solving problems, testing improvements, or refining how things work and they’re on your W-2 payroll, — their time may qualify.

How To Maximize Payroll-Based Tax credits:

  • Track time accurately across qualifying projects. Use payroll systems (like Gusto, ADP, or QuickBooks) that support job-costing or project tracking
  • Assign R&D-specific payroll codes or time categories
  • Document tasks that meet IRS criteria
  • Leverage both federal and state-level opportunities - many can be claimed concurrently

Don't leave money on the table. This is one of the most common, and costly, missed opportunities we see. For startups with no income tax liability, the credit can offset payroll taxes directly,a significant cash flow advantage.

Startup Benefits: Offset Payroll Taxes

Early-stage businesses often assume they can’t benefit because they don’t yet owe income taxes. That’s not true.

If your company has less than $5 million in gross receipts and is under five years old, you can apply the credit to your payroll taxes instead — up to $500,000 per year.

Real World Example

A pre-revenue SaaS startup with $400,000 in developer wages might qualify for a $40,000 credit — a huge cash flow boost that offsets their quarterly payroll tax liabilities.

Why is the R&D credit sometimes overlooked?

Here’s why many companies don’t take advantage of it:

  • Myth: "We’re not a research company."
  • Reality: Innovation doesn’t have to be groundbreaking, routine improvements count.
  • Myth: "We don’t have a lab."
  • Reality: If you're solving problems, writing code, or improving internal systems, you might qualify.
“If your team is innovating, even internally, you’re likely doing R&D without realizing it.” - Deborah Pallasch

How Do I Know If I Qualify? Here’s a quick Test

Ask yourself:

  • Are we improving or creating a product, process, or technology?
  • Are employees spending time on testing, development, or refinement?
  • Do we document our technical processes and expenses?
  • Are our gross receipts less than $5 million?

If you answered yes to any of these, it’s worth exploring further.

Payroll Tax Credit FAQs 

  1. What types of industries qualify for the R&D tax credit?
    Any industry (manufacturing, construction, software, biotech, even food processing) can qualify if it involves innovation or process improvement.
  2. Can startups benefit from the R&D tax credit if they aren’t profitable?
    Yes, startups can use the credit to offset payroll taxes – up to $500,000 annually
  3. What Type of Documentation is Needed?
    You need time tracking, technical documentation, and cost breakdowns to support your claim.
  4. Can I claim both federal and state credits?
    Yes, many states offer an R&D tax credit in addition to the federal version, and both can be claimed concurrently.
Let's Connect

Ready to Unlock Savings Hiding in Your Payroll?

Don’t let innovation go un-rewarded! We can help you determine your eligibility and take a closer look at your payroll.

Deborah Pallasch, Partner, Tax Services Group

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