Author:
R&D Tax Advisors
Role:
CPA
Publish Date:
Oct 31, 2025
The Question
“Should my CPA handle the R&D tax credit, or is it better to use a specialist firm?”
It’s a reasonable question — and one almost every founder or CFO asks once they learn about the credit.
Both CPAs and R&D specialists can prepare R&D studies, but the scope, depth, and purpose of their work often differ significantly.
The Short Answer
Both play important roles, but they serve different functions:
CPAs focus on compliance — ensuring the credit is calculated correctly and filed properly with your tax return.
R&D specialists focus on qualification and documentation — identifying what work actually qualifies under Section 41 and building the audit-ready support behind it.
In many cases, the best outcome comes when both work together.
The Deep Dive
1. What CPAs Do Well
Most companies already rely on a CPA firm for their income tax compliance. These professionals understand your entity structure, your financials, and your broader tax position — which is essential when applying credits.
Strengths:
Deep knowledge of your overall tax picture and timing of credits.
Familiarity with prior-year filings and ownership structures.
Ability to integrate the credit efficiently into your return.
Limitations:
R&D credits are a highly specialized area of the tax code, and not all CPAs focus on them regularly.
Heavy workloads during busy seasons often limit how much time can be spent on documentation and technical interviews.
Some firms rely on client-provided estimates or software templates that don’t fully meet IRS expectations for substantiation.
Best fit: Companies with relatively straightforward development activities or smaller credit amounts that need a compliant filing but face low audit exposure.
2. What R&D Specialists Do Well
R&D specialists dedicate their work exclusively to Section 41 studies. They combine tax knowledge with technical interviews and documentation review — often collaborating with engineering, product, or operations teams directly.
Strengths:
Deep familiarity with the IRS four-part test and industry-specific qualification nuances.
Focus on qualitative documentation — the “why” behind each project’s eligibility.
Ability to identify and substantiate credits across multiple years and states.
Experience supporting claims under audit, where the details matter most.
Limitations:
Specialists generally don’t prepare or sign the corporate tax return — they provide the study and support for your CPA to attach.
The quality among providers varies widely; due diligence is critical.
Best fit: Companies with multiple active development projects, complex ownership structures, or material R&D spend seeking audit-ready documentation and long-term credit strategy.
3. Why Collaboration Produces the Best Results
The most sustainable approach often combines the strengths of both.
A well-prepared R&D study by a specialist feeds directly into a CPA’s compliance process. The CPA ensures it integrates properly into the tax return; the specialist ensures the numbers are defensible and supported.
This separation of roles also protects both sides — the CPA from overextending into unfamiliar territory, and the company from weak or unsupported documentation.
When evaluating options, ask:
How will the specialist coordinate with my CPA?
Who performs the technical interviews and documentation?
What level of audit support is included?
How are adjustments or state credits handled?
4. How the Decision Scales with Company Size
Company Profile | Recommended Approach | Reasoning |
|---|---|---|
Startup (< $1M in R&D spend) | CPA or automated tool | Simpler structure and lower credit justify a lightweight process. |
Growth-stage tech (5–50 engineers) | Specialist + CPA collaboration | Enough complexity to need strong documentation, but still efficient coordination. |
Established mid-market (50–200 engineers) | Dedicated R&D firm or hybrid model | Scale demands a consistent methodology across multiple projects and years. |
Enterprise (> 200 engineers) | Big Four or large consulting team | Complex multi-state, multi-entity structures and audit exposure require full-scale studies. |
The Takeaway
You don’t need to choose between a CPA and an R&D specialist — you need to understand what each brings.
A CPA ensures your credit is filed and integrated correctly; a specialist ensures it’s qualified, documented, and defensible.
For most growing technology companies, collaboration is the ideal path: one partner handles the compliance, and the other ensures the credit stands on solid ground.
