Strategic Reform of the Iowa Research Activities Tax Credit: Restoring Economic Competitiveness through the Reinstatement of the Substantially All Rule for Small and Medium-Sized Enterprises

Introduction

The state of Iowa has historically positioned itself as a premier destination for industrial innovation, leveraging a sophisticated framework of tax incentives to attract and retain high-growth industries in advanced manufacturing, bioscience, and software engineering. For nearly four decades, the Research Activities Credit (RAC) served as the primary fiscal mechanism for incentivizing private-sector investment in experimentation and technical discovery.¹ However, recent legislative overhauls, specifically those enacted through House File 2317 and Senate File 657, have fundamentally altered this landscape.

The most technically significant and operationally burdensome of these changes is the effective repeal of the federal “Substantially All” rule, which previously allowed for a reasonable 80% threshold for qualifying research activities and wages.¹ By moving to a 100% threshold—requiring that every activity and every dollar of a researcher’s wages be tied exclusively to a process of experimentation—the state has inadvertently created a barrier to entry for small to medium-sized businesses (SMBs) that lack the administrative capacity to maintain such granular documentation.¹ This report analyzes the technical, fiscal, and economic implications of this policy shift and proposes structural solutions to restore Iowa’s competitive standing while maintaining rigorous program integrity.

The Evolution of the Iowa Research Activities Credit Framework

The Iowa Research Activities Credit was established in 1985 as a mirror to the federal research and experimentation credit, designed to provide a 6.5% refundable incentive for qualified research expenditures (QREs) incurred within the state’s borders.² For much of its history, the credit was an “entitlement” program, meaning any business meeting the statutory requirements could claim the credit on its tax return without prior state approval.⁴ This framework was highly successful in encouraging firms like Deere & Company and RTX Corporation to center their global R&D activities in Iowa.⁶ However, the program’s success also led to significant fiscal outlays, with claims reaching approximately $77.6 million in fiscal year 2024.⁷

Beginning in 2017, the legislature began a process of narrowing the credit’s scope, limiting eligibility to specific targeted industries: manufacturing, life sciences, agriscience, software engineering, and aviation or aerospace.¹ These reforms excluded sectors such as retail, wholesale, and various types of contracting and professional services, ensuring that the state’s subsidy was directed toward high-value technical innovation rather than routine business operations.⁸ Despite these limitations, the fundamental calculation of the credit remained aligned with Internal Revenue Code (IRC) Section 41, providing a predictable and stable environment for researchers.²

The enactment of House File 2317 in 2022 represented a paradigm shift. In addition to phasing down individual and corporate tax rates, the bill introduced revenue-raising measures that targeted the RAC.¹ These included mandatory alignment with the federal alternative simplified credit (ASC) method, the incremental reduction of refundability for excess credits, and the systematic phase-out of supply expenses from the QRE base.¹ Most critically, the law explicitly detached the Iowa credit from the federal “Substantially All” rule for determining qualified services.¹¹ This was followed by Senate File 657, which will fully replace the legacy RAC with a new, capped, and application-based “R&D Tax Credit Program” in 2026.⁷

Table 1: Evolution of the Iowa R&D Incentive Structure

Source: 1

Technical Analysis of the “Substantially All” Rule and its Repeal

The “Substantially All” rule is a cornerstone of the federal R&D tax credit regime, primarily articulated in IRC Section 41(b)(2)(B) and Treasury Regulation 1.41-2(d)(2).¹ The rule serves two distinct but related purposes in the calculation of research credits: the qualification of activities and the qualification of wages.

In the context of activities, the rule applies to the “Process of Experimentation” (PoE) test, which is the final and often most scrutinized element of the mandatory four-part test for qualified research.⁴ To meet this test, a project must demonstrate that “substantially all”—interpreted as 80% or more—of its activities constitute elements of a process designed to evaluate alternatives and resolve technical uncertainties.⁴ This 80% threshold provides a pragmatic “Safe Harbor,” acknowledging that even the most rigorous scientific inquiry involves a certain amount of non-experimental documentation, administrative planning, and routine data management that is inextricably linked to the core research.¹³

In the context of wages, the rule provides a “cliff effect” for the inclusion of employee compensation. If an employee performs qualified research services—which include direct research, direct supervision, or direct support—for 80% or more of their working time, the employer is permitted to claim 100% of that employee’s wages as QREs.¹³ If the time spent on qualified services falls below the 80% threshold, the employer may only claim the actual percentage of the employee’s time dedicated to research.¹³

The Mechanism of the Iowa Repeal

The repeal of this rule in Iowa was achieved through specific amendments to Iowa Code Section 422.10, which now states that the “substantially all” rule for determining qualified services as described in the IRC and Treasury Regulations “does not apply”.¹¹ This detachment from federal conformity forces Iowa researchers into a binary “100% requirement”.¹ Under this new standard, any time spent by an engineer or scientist on non-qualified tasks—such as attending a general business meeting, completing human resources training, or participating in a sales presentation—must be meticulously carved out of the credit calculation.¹

For SMBs in Iowa, this change is not merely a matter of arithmetic but of administrative survival. In a small manufacturing firm or a growth-stage biotech startup, researchers and technical leads are rarely siloed; they often perform “integrated” roles that span R&D, production oversight, and customer-facing technical support.⁴ The 100% rule effectively penalizes these firms for having lean, efficient workforces, as the documentation required to prove 100% compliance for each researcher is often more expensive than the value of the credit itself.¹⁵

The Documentation Gap and Audit Risk

The 100% threshold necessitates “forensic-level validation” and contemporaneous documentation of every hour of a researcher’s year.¹⁷ While large entities like Deere & Company possess the resources to implement automated, project-based time-tracking systems across their 432 reporting businesses, an SMB typically relies on periodic time studies or broad allocation models.⁴ The Iowa Department of Revenue (IDR) guidance emphasizes that only research that is “Experimental,” “Undertaken to discover information that is technological in nature,” and “Aimed at the development of a new product” qualifies.⁶ Without the 80% safe harbor, any lack of precision in documentation results in the immediate disqualification of that portion of the claim, creating a significant audit risk for firms that are already operating on thin margins.⁴

Table 2: Impact of Repeal on Expenditure Categories

Source: 1

Economic Implications for Iowa’s Small to Medium Business Ecosystem

Small to medium-sized businesses are the primary drivers of diversification in Iowa’s innovation economy. While the 2025 Annual Report on the Research Activities Tax Credit highlights that twelve large companies earned nearly 70% of the total credits, it also notes that there were 1,012 individual claims—primarily from pass-through entities such as LLCs and S-corporations—totaling roughly $3.5 million.⁶ These claims represent the “seed corn” of Iowa’s future industry leaders. The repeal of the “Substantially All” rule affects these entities disproportionately through three distinct economic pressures: the “Documentation Tax,” the “Liquidity Squeeze,” and the “Competitive Brain Drain.”

The Documentation Tax

For an SMB, the compliance cost associated with the R&D credit is effectively a fixed cost that does not scale perfectly with the size of the credit. By moving to a 100% threshold, Iowa has increased this “Documentation Tax”.¹⁵ An SMB claiming $50,000 in credits must now maintain the same level of granular documentation as a firm claiming $5,000,000. Many small firms, particularly those in the software engineering and agriscience sectors in Iowa City or Ames, may find that the internal labor costs required to track 100% of their team’s time to the “Process of Experimentation” exceeds the 3.5% to 6.5% benefit provided by the credit.⁷ This leads to “non-take-up,” where eligible firms simply abandon the credit, effectively raising their cost of doing business in Iowa.

The Liquidity Squeeze

The repeal of the 80% rule does not exist in a vacuum; it is part of a broader “liquidity squeeze” enacted by HF 2317 and SF 657. The systematic reduction of the refundable portion of the credit—from 100% of the excess credit to a projected 50% by 2027—is particularly damaging to startups that are not yet profitable.¹ For these pre-revenue firms, the refundable credit is often their only source of non-dilutive capital to fund prototypes and iterative testing.¹² When the 100% experimentation rule is combined with the supply expense phase-out (which drops to 0% by 2027), the “effective value” of the Iowa R&D credit for a capital-intensive manufacturing or biotech SMB may drop by more than half.¹

Competitive Brain Drain and Regional Relocation

The importance of a tax incentive often depends on its existence relative to other states.¹⁹ If Iowa removes or significantly devalues an incentive that is provided in neighboring states, businesses with mobile R&D operations may relocate.¹⁹ Minnesota recently introduced partial refundability for its R&D credit, making it significantly more valuable for startups in loss positions.¹⁵ Michigan has also enacted a new state R&D credit to compete for technology and manufacturing investment.¹⁵

Iowa’s move toward a 100% threshold makes it an outlier in the Midwest. Most states maintain conformity with the federal 80% “Substantially All” rule to ensure administrative ease for their taxpayers.⁴ If an Iowa-based software firm in the “Silicon Prairie” corridor finds that the compliance burden of the Iowa credit is too high, but the federal credit remains valuable, they may choose to move their research team to a state that offers easier conformity, taking high-wage jobs and payroll tax revenue with them.¹⁵

Proposed Solution 1: Reinstating a Tiered Statutory “Substantially All” Rule for SMBs

The most effective and direct solution to the current policy crisis is for the Iowa legislature to amend Iowa Code Section 422.10 to reinstate the 80% “Substantially All” rule specifically for small and medium-sized businesses. This tiered approach acknowledges that the state’s fiscal concerns were primarily driven by large-scale claimants while providing necessary relief to the smaller innovators who are the focus of Iowa’s economic development strategy.

Defining the SMB Tier for Policy Reinstatement

To implement this change, the legislature should adopt a clear, objective definition for eligible SMBs. Drawing on existing Iowa Code frameworks, such as those used in the “High Quality Jobs” program or the “Seed Investor Tax Credit,” the state could define an SMB as any business with annual gross revenues of $50 million or less.⁶ Alternatively, the state could use an employment-based threshold, such as firms with fewer than 500 Iowa-based employees.

For entities falling within this tier, the statutory language would be amended to explicitly re-adopt IRC Section 41(b)(2)(B) and Treasury Regulation 1.41-2(d)(2) for the purposes of the Iowa credit.¹¹ This would allow these firms to once again claim 100% of an employee’s wages if that employee spends at least 80% of their time on qualified services.¹³

Benefits of a Tiered Reinstatement

A tiered reinstatement solves the “Documentation Tax” problem without significantly impacting the revenue-raising goals of HF 2317. Because the vast majority of the credit’s fiscal impact is concentrated in a dozen large firms (who would remain subject to the 100% rule), the cost to the general fund of providing relief to the 1,000+ SMB claimants would be relatively minor.⁶ At the same time, it provides an “on-ramp” for innovation, encouraging small firms to invest in R&D without the fear of a compliance-driven audit trap.⁴ This tiering would also align with other state models, such as Michigan’s, which provides different credit caps and rates based on company size.¹⁵

Table 3: Proposed Tiered Framework

Source: 6

Proposed Solution 2: Administrative “Safe Harbor” through Professional CPA Certification

A second solution, which could be implemented in tandem with or as an alternative to statutory tiering, involves the creation of an administrative “Safe Harbor.” This solution leverages the existing requirement in Senate File 657 that all 2026 R&D program applicants hire a Certified Public Accountant (CPA) to review and verify their claimed expenses.⁷

Implementing the “Substantial Compliance” Certification

The Iowa Economic Development Authority (IEDA), in consultation with the Department of Revenue, should issue administrative rules that allow a CPA to certify a business’s “Substantial Compliance” with the Process of Experimentation.⁷ Under this model, if a CPA conducts a rigorous audit following a state-approved protocol—including a review of technical uncertainty, project logs, and time sampling—and finds that 80% or more of the project’s activities are experimental, the state would accept the project as 100% qualified for the purposes of the Iowa credit.⁴

This shifts the burden of granular “minute-by-minute” verification from the taxpayer and the state auditors to a qualified third-party professional who is already mandated to be part of the process.⁷ By allowing the CPA to use statistical sampling and professional judgment rather than requiring 100% documentation for every researcher, Iowa can significantly reduce the compliance burden on its SMBs while maintaining a high level of financial rigor.¹⁴

Standardizing Professional Due Diligence

To prevent the emergence of “bad providers” or “aggressive vendors” who might exploit a “Substantial Compliance” standard, the IEDA must establish strict “Multi-Disciplinary Due Diligence” frameworks.¹⁷ Certification would require:

• Dual Professional Sign-off: Both a CPA (for financial vetting) and a qualified engineer or technical expert (for eligibility vetting) must review the claim.¹⁷
• Contemporaneous Documentation Verification: The certifying professional must verify that documentation was created at the time the research occurred, not reconstructed after the fact.⁴
• Site Visit Requirement: For claims exceeding a certain threshold, the certifying professional must perform an on-site visit to confirm the existence of experimental models, prototypes, or testing facilities.²³

Strategy for Implementation: Balancing Benefit and Integrity

The successful implementation of these policy changes requires a dual focus on maximizing the benefit for legitimate SMBs while aggressively preventing fraud and wastage. As Iowa moves to an application-based program in 2026, it has a unique opportunity to design “Program Integrity” into the very fabric of the new R&D Tax Credit Program.⁷

Preventing Fraud and Wastage through Enhanced Oversight

Fraud in R&D tax credits typically manifests in two ways: the “inflation of ineligible costs” (e.g., claiming routine maintenance as R&D) and the “claiming of non-existent research”.¹⁷ To combat this, the IEDA should adopt the following “Gold Standard” strategies ²⁴:

• Fraud Risk Assessments: Before each annual application cycle (due January 31st), the IEDA should conduct a risk assessment to identify emerging “scams” or sectors with a high frequency of improper claims.⁷
• Debarment and Penalties: Businesses, CPAs, or tax brokers found to have submitted fraudulent or intentionally inflated claims should be subject to immediate debarment from all Iowa economic development programs and face prosecution for perjury.¹⁷
• Mandatory Reporting of IP Ownership: A key lesson from recent IRS scrutiny is that research “ownership” and “financial risk” are critical to qualification.²¹ Iowa applications should require explicit disclosure of who owns the intellectual property and who bears the expense if the research fails.²¹

Implementation for SMB Benefit

To ensure the changes truly benefit SMBs, the application process must be streamlined. The IEDA should maintain an online portal that allows for “Proactive Engagement” rather than “Passive Claiming”.⁷ For SMBs that are already certified (a certification that lasts five years under SF 657), the annual application should focus on changes in expenditure levels and the outcomes of the research (jobs created, patents filed) rather than a de novo re-justification of their entire business model.⁷

Cost Analysis and the Future Benefit Paradigm

The fiscal impact of reinstating the “Substantially All” rule for SMBs must be viewed as an investment in a depreciable but high-yield asset: Iowa’s intellectual capital. While a static fiscal analysis might show a direct reduction in tax revenue, a dynamic analysis reveals that the initial cost outlay will be more than recovered through the “Innovation Multiplier.”

Initial Cost Outlay Modeling

Based on the 2025 Annual Report, SMB claims (individuals and pass-throughs) total approximately $3.5 million per year under the current, more restrictive rules.⁶ If the “Substantially All” 80% rule were reinstated for these entities, and the “Documentation Tax” were lowered to encourage take-up, total SMB claims might rise to $7 million to $10 million annually.⁶ This represents a relatively small fraction of the $40 million cap scheduled for 2026 and an even smaller fraction of the $1.2 billion in net general fund revenue reductions estimated from other parts of HF 2317.⁷

Framing Future Benefits and ROI

The return on investment (ROI) for R&D tax credits is realized through three primary channels: the “Fiscal Multiplier,” the “Leveraging of Private Capital,” and the “Sector Stability Benefit.”

• The Fiscal Multiplier: Programs like SNAP have a known economic multiplier of 1.54, but high-tech R&D credits often exceed this due to the high wages of the jobs they support.²⁸ The 2025 report shows that R&D wages in Iowa totaled $1.55 billion.⁶ Even a 1% increase in this wage base through better incentives would generate significantly more in payroll tax, sales tax, and local economic activity than the cost of the credit itself.⁶
• Leveraging Private Capital: Iowa’s “Manufacturing 4.0” grants have demonstrated a leverage ratio of 3-to-1 ($9.3M in grants leading to $37M in total capital investment).³⁰ By restoring the “Substantially All” rule, Iowa lowers the “risk” of R&D for small firms, encouraging them to commit private capital that would otherwise remain on the sidelines or be invested in other states.³⁰
• Sector Stability: R&D credits reduce the “liabilities” of innovative firms, helping them survive downturns and reorganize without cutting their core technical staff.²⁹ This stability ensures that Iowa’s “Agriscience” and “Bioscience” clusters remain intact, providing a foundation for future growth that pays for the program many times over through sustained corporate tax receipts.⁵

Table 4: Economic ROI Projections

Source: 6

The Imperative for Change: Negative Consequences of Inaction

The current trajectory of Iowa’s R&D tax policy is one of “managed decline” for the small business sector. While large corporations will continue to claim the lion’s share of the credit despite the 100% threshold, the “cliff effect” created by the repeal of the “Substantially All” rule will lead to several severe negative consequences if not corrected immediately.

Erosion of the “Silicon Prairie” Ecosystem

Innovation ecosystems are fragile and depend on a critical mass of talent and capital. The move to a 100% experimentation threshold, combined with the discretionary nature of the 2026 application-based program, creates “regime uncertainty”.⁷ If small software engineering or bioscience firms cannot predict their credit amount—due to both the pro-rata allocation and the 100% documentation hurdle—they will stop including the credit in their financial planning.⁷ This leads to a gradual erosion of the “Silicon Prairie” as firms either close or relocate to states like Minnesota, which are moving in the opposite direction by increasing refundability and accessibility.¹⁵

The Stifling of “Manufacturing 4.0” Integration

Iowa is currently making a major push to help its manufacturers integrate “Smart Technology” to remain globally competitive.³⁰ This transition requires iterative testing and a process of experimentation that is often performed by existing shop-floor engineers.²⁶ Under the 100% rule, these engineers—who spend a portion of their time on routine production—may no longer qualify for the credit, or the cost to “carve out” their non-research time may be prohibitive.¹ This effectively taxes the very innovation the “Manufacturing 4.0” initiative seeks to encourage, creating a internal policy contradiction that hampers state economic goals.

Increased Litigation and Administrative Friction

Finally, the 100% rule is a recipe for administrative conflict. In the absence of an 80% safe harbor, every audit by the Department of Revenue becomes an exercise in “splitting hairs” over how a researcher spent their time.⁴ This leads to increased litigation costs for both the state and the taxpayer and wastes the expertise of state-employed scientists and engineers on administrative adjudication rather than technical advancement.⁵

Conclusion: A Path Forward for Iowa’s Innovation Economy

The repeal of the “Substantially All” rule in Iowa was a technical change with massive operational consequences. While the legislature’s intent to protect the general fund and target high-value innovation was sound, the resulting 100% threshold has created an “unusually high bar” that threatens to alienate the state’s most promising small to medium-sized businesses. To ensure that Iowa remains a leader in the industrial and biological sciences, a course correction is necessary.

By implementing a tiered statutory reinstatement of the 80% rule for SMBs and creating an administrative “Safe Harbor” through professional CPA certification, Iowa can restore its competitive edge. These solutions provide the necessary balance: they protect the state’s fiscal position by maintaining the high bar for the largest claimants, while providing the administrative flexibility required for smaller, high-growth firms to innovate. When paired with rigorous fraud prevention and a focus on “Substantial Rights” and ownership, these reforms will ensure that the Iowa Research Activities Tax Credit remains a robust, efficient, and defensible driver of economic prosperity. The initial revenue outlay required for these changes will be more than compensated by the long-term growth of a diversified, high-wage technical workforce and a stabilized manufacturing base that is prepared for the next industrial revolution.

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