NIH, DOE, and DoD Grant Accounting
Comprehensive Compliance and Financial Stewardship for Federally Funded Research
Protect Your Funding. Strengthen Your Reporting. Build a Culture of Compliance.
Winning a federal grant is a milestone—but managing one requires meticulous compliance and financial discipline. The NIH, DOE, and DoD each have their own reporting systems, indirect cost standards, and audit requirements that must align with Uniform Guidance (2 CFR 200) and agency-specific supplements.
At Peter Witts CPA PC, we help research organizations, universities, and private contractors maintain grant accounting systems that are both compliant and operationally efficient. From pre-award budget setup to post-award closeout, we ensure every cost is allowable, allocable, and properly documented—so you can focus on research, not red tape.
Why Grant Accounting Is Different from Contract Accounting
Federal grants operate under
assistance rules, not
acquisition. That means the objectives are collaborative, but the fiscal responsibility is uncompromising.
Compliance is governed primarily by
2 CFR 200 (Uniform Guidance), with agency-specific policies layered on top:
- NIH Grants Policy Statement (GPS)
- DOE Financial Assistance Regulations (10 CFR 600)
- DoD Research and Related (R&R) Policy Guide
- Each introduces unique nuances—rebudgeting thresholds, indirect cost restrictions, participant support rules, and drawdown requirements.
Our team translates these policies into practical systems that withstand Single Audits, DCAA, and agency-specific reviews.
Pre-Award Budget & Indirect Rate Setup
Before award acceptance, your financial structure must already reflect compliant practices. We provide:
- Budget formulation aligned with 2 CFR 200 §200.308 (revision of budget and program plans).
- Determination of F&A (Facilities & Administrative) or indirect cost rates—whether negotiated (NICRA) or de minimis.
- Fringe rate development consistent with institutional or sponsor policy.
- Pre-award risk assessments and internal control design per §200.302(b).
Early alignment prevents later disallowances and simplifies post-award reporting.
Post-Award Grant Accounting & Administration
Once funding begins, daily activity must meet Uniform Guidance standards for
allowability (§200.403),
allocability (§200.405), and
consistency (§200.412–§200.414).
Our post-award support includes:
- Grant-level general ledger setup and monthly reconciliations.
- Labor distribution and effort certification compliant with §200.430.
- Expense review to exclude unallowables (entertainment, lobbying, alcohol).
- Indirect cost application consistent with approved rate agreement.
- Budget-to-actual tracking and variance analysis.
- PMS and ACM$ (NIH) drawdown preparation and submission.
We keep your ledgers, drawdowns, and progress reports synchronized and audit-ready.
Effort Reporting & Payroll Compliance
Personnel costs often represent the majority of federal grant expenditures. We help implement and monitor:
- Time and effort certification systems meeting Uniform Guidance §200.430(i) standards.
- Integrated labor distribution between direct, indirect, and cost-share accounts.
- Fringe benefit allocation consistent with rate agreements.
- Documentation sufficient for DCAA or Single-Audit verification.
Our frameworks stand up to scrutiny from both auditors and institutional compliance officers.
Subrecipient Monitoring & Cost Share Tracking
Under §200.331–§200.332, prime recipients are responsible for subrecipient oversight. We design processes to:
- Perform pre-award risk assessments and subrecipient evaluations.
- Review invoices for allowability and performance documentation.
- Track cost-share commitments and third-party contributions.
- Maintain audit-ready records for both prime and subrecipient expenditures.
These controls safeguard your funding and fulfill your stewardship obligations.
Indirect Cost Rate Proposals (F&A and NICRA)
We prepare and negotiate
F&A rate proposals under
Appendix III to 2 CFR 200 and
NICRA submissions for research contractors subject to DCAA review.
Services include:
- Pool and base composition following FAR 31.201-2/-4 and CAS 401/402.
- Calculation of facilities depreciation and capital cost of money (CAS 414/417).
- Documentation packages and reconciliations for cognizant agency submission.
- Rate projection and impact modeling for future year budgets.
With properly structured indirect rates, you maintain compliance and recover your full share of allowable costs.
Drawdowns, Reporting & Closeout
Every agency requires different reporting cadences and systems. We manage:
- NIH eRA Commons / ACM$ and DOE PMS drawdowns with reconciliation to expenditures.
- Quarterly financial reports (SF-425 / FFR).
- Final financial and technical closeouts per §200.344.
- Audit preparation for Single Audits (§200 Subpart F) or DCAA incurred-cost reviews.
We ensure each grant’s life cycle—budget, drawdown, and closeout—flows cleanly and defensibly.
Your Partner in Scientific and Financial Integrity. Compliance shouldn’t compete with discovery.
With Peter Witts CPA PC, you gain a financial partner who understands the science and the statutes—so your research stays funded, compliant, and audit-ready from day one through final report.
Frequently Asked Questions
What is “government contract accounting,” and how is it different from regular accounting?
Government contract accounting involves following specific federal rules, standards, and compliance requirements (e.g. cost allowability, audit readiness, indirect rates, DCAA standards). Unlike general accounting, your financial systems need to withstand audits, cost proposals, and strict oversight. We structure your accounting and reporting so you stay compliant and reduce risk.Do I need to worry about DCAA audit compliance?
If you hold or are bidding on U.S. federal contracts (especially cost-reimbursable, time & materials, or fixed price with cost elements), the Defense Contract Audit Agency (DCAA) may audit your accounting systems. We can help you build or review systems so you pass audits when they arrive.Can you help with indirect cost rates, cost proposals, and incurred cost submissions?
Yes — we support designing indirect cost rate structures, preparing cost proposals, and submitting incurred cost reports. These are critical tasks in government contracting, and we ensure your supporting records align with regulatory expectations.How much experience do you have in the federal contracting space?
Peter Witts CPA PC has over 36 years of experience in government contract accounting, including first-hand DCAA knowledge. We’ve worked with clients across DoD, NIH, DOE, and other agencies, helping them navigate the compliance landscape.What kind of businesses or projects do you work with?
We work primarily with companies engaged in federal contracts or grants (especially research, development, support services). If your business isn’t in that space, we’ll help you determine whether our services are the right fit or recommend alternatives.How do I get started with you?
You can schedule a free consultation via our website. During that call we’ll explore your current standing, challenges, and needs, and map out how we might support you. (Then we’ll formalize scope, pricing, and next steps.)What should I provide for an initial assessment?
Financial statements, accounting policies, prior audits (if any), contracts and grant agreements, cost accounting structure, payroll records, indirect cost allocations, and any compliance documents. We’ll review what you have, identify gaps, and propose next steps.How often will we interact / how do you deliver services?
That depends on the scope. For outsourced accounting, we could work on a monthly or quarterly basis. For compliance or audits, we may engage more intensively. We'll agree up front on communication frequency, deliverables, and review cycles.What are your fees or how is billing handled?
Our fees are fixed monthly fees and depend on the complexity and scope of your work — number of contracts, volume of accounting entries, compliance risk, etc. We’ll provide a proposal after our initial assessment. We only work on an hourly basis for audit support services for audits relating to government contracts or grants conducted by government agencies or outside CPA firms.What if my business is outside of your specialization—can you still help?
At Peter Witts CPA PC, we focus exclusively on our core strength: federal contract and grant compliance. We serve businesses operating within the government contracts and grants space, offering specialized outsourced accounting and tax services tailored to the unique requirements of this industry. This is our sole focus — we don’t try to be everything to everyone. Our expertise is deep, not broad, and it’s dedicated to helping government contractors navigate complex compliance and maximize their opportunities.What happens if there's a federal audit or examination?
We support audit responses, documentation requests, and work with your team to ensure you respond properly. Because we build systems with compliance in mind, we aim to minimize surprises and help you maintain defensible records.How do you keep up with changing federal regulations and compliance standards?
We continuously monitor federal regulatory updates (DCAA rules, OMB circulars, FAR/DFARS, audit guidelines) so our clients’ accounting systems remain in alignment with best practices and compliance requirements.
