NYC DOHMH Grant Compliance: A 2026 Guide for Contractors

If your organization holds a DOHMH service contract, the compliance load is heavier than most other NYC agency work because the dollars are usually federal underneath. CDC pass-through for Public Health Emergency Preparedness, HRSA pass-through for Ryan White and 330-funded clinical work, CMS pass-through for Medicaid waivers, and SAMHSA pass-through for behavioral health all flow through DOHMH program areas before they reach contractors. That layering is the part that most finance staff underestimate the first time through an audit.

This guide is the layer above what’s already on the DOHMH program page and the contract-specific RFP. It assumes you already know which program area you’re working in, who your DOHMH program manager is, and which version of HHS Accelerator you submit through. What it covers is the structure: how Article 6 community-health rules, Article 28 facility rules, federal Uniform Guidance, NYC procurement, and program-specific reporting fit together.

The Stack: Five Compliance Frames That Apply Simultaneously

A DOHMH-funded program does not live under one rulebook. It lives under five, and they apply concurrently.

• Federal Uniform Guidance (2 CFR Part 200). When DOHMH passes federal dollars through to you, every applicable subpart applies — cost principles in Subpart E, procurement standards in Subpart D, audit requirements in Subpart F. The Uniform Guidance practical guide walks through the structure if you’re new to it.
• Federal program-specific rules. CDC, HRSA, CMS, and SAMHSA each layer program-specific reporting on top of the cross-cutting Uniform Guidance.
• NYC Charter and Procurement Policy Board rules. NYC contracts are registered with the Comptroller, signed under PPB rules, and invoiced through PassPort or HHS Accelerator.
• NY State public health law (Articles 6 and 28). Article 6 frames how city health departments operate; Article 28 governs facility licensure where programs run inside DTCs or hospitals.
• DOHMH program division rules. Each DOHMH division publishes its own contractor handbook with reporting templates, deliverable definitions, and data-submission requirements.

A finding in any one frame can disallow costs across the others. The audit posture is to keep evidence files that can satisfy each frame independently and that reconcile against each other.

Article 6 in Practice

Article 6 of the New York Public Health Law authorizes county and city health departments. For NYC, it is the legal foundation under which DOHMH operates as a city health department. Most contractors don’t interact with Article 6 directly — but its structure shapes the kinds of community health services DOHMH funds. Health education, communicable disease surveillance, environmental health inspections, maternal and child health programs, and chronic disease prevention are the historical Article 6 categories, and they remain DOHMH’s core program structure.

For a contractor, the practical implication is that DOHMH’s program managers think in those buckets. A program proposal framed against the Article 6 categories — health education, surveillance, environmental health, MCH, chronic disease — reads cleanly to a DOHMH program officer. A proposal framed in language pulled from a different funder’s RFP often does not.

Article 6 also shapes how DOHMH’s program data integrates with NY State DOH reporting. State surveillance data flows up under Article 6 authority. If your program contributes to that data — communicable disease reporting, lead exposure, immunization, environmental health complaints — your data submission obligations are not optional and are not satisfied by the DOHMH grant invoice alone.

Article 28 in Practice

Article 28 is where compliance gets dense. If your DOHMH-funded program runs inside a diagnostic and treatment center (DTC), a hospital, or another Article 28 facility, you live under both the DOHMH contract and the New York State DOH facility licensure regime.

The audit-relevant points:

• Cost reports. Article 28 facilities file annual cost reports to NY State DOH (the Institutional Cost Report). The data on the ICR must reconcile to the DOHMH contract budget where they overlap. A grant-funded clinic that reports a different staffing FTE count on its ICR than on its DOHMH expenditure report is creating an audit finding waiting to happen.
• Medical record retention. Article 28 record retention schedules generally exceed the federal Uniform Guidance three-year minimum. Pediatric records are retained longer, often through the patient reaching age of majority plus a state-defined number of years. When DOHMH contracts reference clinical records, the longer Article 28 retention rule controls.
• Quality assurance. Article 28 facilities operate under quality-assurance committee structures. DOHMH contract quality measures need to flow through the QA committee, not parallel to it.
• Billing. Programs in Article 28 facilities often bill Medicaid for the same encounters that contribute to DOHMH performance metrics. The accounting must clearly separate the two revenue streams to avoid the Medicaid-payer-of-last-resort problem and to keep the federal pass-through math clean.

If your organization holds DOHMH funding for any program inside an Article 28 facility, your finance and clinical operations teams need a coordinated workflow. The cost principles laid out in 2 CFR 200 Subpart E become the integrating frame; everything else has to roll up to it.

Health Bucks: Documentation Pattern

Health Bucks looks small in budget terms relative to clinical contracts, but it is one of the most-audited DOHMH program areas because the unit cost is low and the documentation chain is long. The compliance pattern that works:

• Maintain a coupon-issuance log per market location with date, market name, batch range of coupon serial numbers, and issuance staff signature.
• Maintain a redemption ledger from each participating market, reconciled to coupon serial numbers and to vendor reimbursements.
• Track demographic data only where DOHMH contractually requires it; over-collection creates a separate set of privacy concerns.
• Reconcile coupons issued to invoiced expenses monthly. The cost of coupon production, distribution staff time, and market support are typically the only allowable expense lines.
• Retain coupon records and reconciliation files for the longer of the contract retention term or six years.

DOHMH spot-checks Health Bucks reconciliations quarterly in many program areas. A clean documentation chain prevents disallowed costs.

NYC Procurement on Top of Federal Procurement

When a DOHMH-funded program needs to buy goods or services with federal pass-through dollars, two procurement frameworks apply at once: NYC PPB and federal Uniform Guidance Subpart D.

The federal procurement methods at 2 CFR 200.320 are: micro-purchase, small purchase (simplified acquisition), sealed bids, competitive proposals, and noncompetitive procurement. Federal thresholds drive when each method is required — a topic covered in detail in the federal procurement thresholds guide.

NYC PPB rules add their own procurement methods and approvals. Where the rules differ, the more restrictive applies. Practical implications:

• A purchase that meets the federal micro-purchase threshold is not automatically compliant with NYC rules; the contractor’s own procurement policy may require quotes at a lower threshold.
• Sole-source justifications need to satisfy both federal noncompetitive procurement criteria and any NYC noncompetitive procurement justification template the contract requires.
• Conflict-of-interest disclosures need to satisfy the federal standards in Subpart D and DOHMH’s own COI policy. Many contractors maintain a single combined disclosure form.

For pass-through contractors that subcontract a portion of the work, the subrecipient monitoring guide covers the additional layer that DOHMH expects you to apply downward to your subrecipients.

Audit Expectations

DOHMH contractors face audit pressure from multiple directions.

• Single Audit. When your federal expenditures across all sources cross the threshold ($750,000 for fiscal years ending before October 1, 2024; $1,000,000 thereafter), you are subject to the Single Audit. The auditor selects major programs based on risk; large DOHMH pass-through contracts are usually in scope as a major program at least once across the audit cycle.
• Comptroller audits. The NYC Comptroller’s office runs contract-specific audits. These tend to focus on procurement documentation, invoicing accuracy, and deliverable evidence.
• DOHMH program audits. DOHMH division-level audits focus on programmatic data integrity — service counts, demographic data, deliverable evidence — and tie those back to invoiced expenses.
• State DOH inspections. Where Article 28 applies, state DOH conducts facility surveys on a separate cadence.

A contractor that has all four audit angles covered tends to share one trait: a single source-of-truth ledger that program data, fiscal data, and deliverable evidence all reconcile back to. The shared ledger is the difference between an audit that finishes in six weeks and one that drags into the next contract year.

Documentation Files to Maintain

The minimum file structure that withstands DOHMH audit cycles:

• Contract and modifications file. Original contract, every registered modification, and the signed cover letters.
• Budget file. Original approved budget, every approved budget modification, and a working budget reconciled to the general ledger monthly.
• Personnel file. Time and effort certifications under 2 CFR 200.430, position descriptions tied to the budget, and credential documentation for any clinical staff.
• Procurement file. Procurement policy, conflict-of-interest disclosures, every solicitation and contract for purchases above the contractor’s quote threshold, and sole-source justifications.
• Programmatic file. Service delivery logs, deliverable evidence, data-submission records, and program quality assurance documentation.
• Subrecipient file. For each subaward: subrecipient risk assessment, executed subaward agreement, monitoring records, and closeout package.
• Audit file. Single Audit reports, audit corrective action plans, and Federal Audit Clearinghouse confirmations.

For broader audit prep across the federal portion of these files, the audit prep checklist and grant compliance checklist cover the full sweep.

Where DOHMH Contractors Get Caught

The recurring findings across DOHMH audit cycles cluster in five categories.

• Time and effort certifications missing or generic. Auditors want signed certifications that reflect actual effort distribution across funding sources, not boilerplate split percentages.
• Procurement undocumented. A purchase made without quotes that should have triggered them, or a sole-source justification written after the fact.
• Budget modifications late or missing. Spending in a category that was reallocated only after the spend occurred.
• Article 28 / DOHMH cost mismatch. Same staff, same patients, two different cost numbers across the ICR and DOHMH expenditure report.
• FFATA subaward reporting missed. Subawards over $30,000 in federal pass-through dollars require monthly FFATA reporting; missed filings show up in Single Audit.

The common single audit findings guide and single audit threshold guide cover the federal angles in more detail.

Software and Workflow Considerations

DOHMH compliance is a documentation-management problem more than an accounting problem. The contractors that handle it well typically have:

• A grant management system that tracks budget, expenditures, and deliverables on the same record. The best grant compliance software listicle covers the category.
• A document repository that maps to the audit file structure above, with retention rules enforced.
• An automated time-and-effort certification workflow.
• Subrecipient monitoring tooling separate from accounts payable.

Spreadsheets work for a single contract. They do not scale to a portfolio of DOHMH contracts plus the federal pass-through reporting, FFATA, Single Audit prep, and Article 28 reconciliation that a multi-contract portfolio implies. The cost of the audit findings that come from poorly tracked compliance dwarfs the software spend.

Where to Start

If you’re picking up DOHMH compliance for the first time:

1. Read the contract — the funding source line and the federal Assistance Listing number tell you which Uniform Guidance subparts apply.
2. Map your DOHMH-funded staff to the Article 6 program categories your contract sits in. That’s the language DOHMH program managers use.
3. If any program runs in an Article 28 facility, schedule a coordination meeting between your finance lead, your clinical lead, and the facility administrator to map cost reconciliation.
4. Build your audit file structure first, before the first invoice. Retrofitting the file structure during a Single Audit is what turns findings into disallowed costs.
5. Calendar every reporting deadline — monthly invoice, quarterly program report, FFATA, annual Single Audit, contract closeout — so they’re owned by a named person on a known cadence.

DOHMH does not award contracts to organizations that look high-risk, and the easiest way to look high-risk is to have a Single Audit with material findings or a Comptroller audit with disallowed costs. The compliance work is the precondition to the next grant cycle. Build the system once and the system carries you forward.

For state-level context, see the New York nonprofit profile. For city-level context including DOHMH and other NYC agencies, see the New York City nonprofit profile.

DEFINITION

Article 6

The chapter of New York State public health law that authorizes county and city health departments and shapes how community-health funding is structured. NYC DOHMH operates under Article 6 alongside its city charter authority.

DEFINITION

Article 28

New York State public health law governing diagnostic and treatment centers, hospitals, and related licensed facilities. Programs delivered inside an Article 28 facility carry licensure obligations on top of any grant terms.

DEFINITION

Health Bucks

DOHMH-issued $2 coupons distributed through farmers markets and community partners that can be used to purchase fresh fruits and vegetables. SNAP recipients earn additional Health Bucks per $5 spent at participating markets.

DEFINITION

PassPort

The NYC procurement and contracting platform run by the Mayor's Office of Contract Services. PassPort handles vendor enrollment, contract registration, invoicing, and audit document submission for most NYC agency contracts including DOHMH.

DEFINITION

HHS Accelerator

NYC's specialized procurement system for health and human services contracts. HHS Accelerator handles solicitations, vendor qualification, and submission of program data for DOHMH and several other NYC agencies.