ISO/IEC 42001:2023 asks for three assessments, and most teams try to squeeze them into one spreadsheet: a gap analysis against clauses 4 to 10 and Annex A, an AI risk assessment under clause 6.1.2, and an AI system impact assessment under clause 6.1.4. Treat them as one exercise and the auditor pulls them apart for you at Stage 2. Treat them as three unrelated projects and you triple the workshops, the registers, and the remediation lists. What works is a single methodology with distinct outputs that share inputs, share a traceability matrix, and feed one remediation plan. This article lays out that methodology end to end: how gap analysis and risk assessment fit together under ISO 42001, how to prepare, the step-by-step process for each, how to merge the outputs into one risk treatment plan, the registers and templates you’ll need, and what a certification body expects to see when you’re done. Why Gap Analysis and Risk Assessment Must Work Together Under ISO 42001 A gap analysis measures distance from the standard. A risk assessment measures exposure from your AI systems. They answer different questions, and ISO 42001 makes them depend on each other in a way ISO 27001 only implies. Clause 6.1.3 requires you to compare the controls you select through risk treatment against Annex A, and to justify any Annex A control you leave out in the Statement of Applicability (SoA). So your Annex A gap analysis has no defensible baseline until the risk assessment tells you which controls you need. Run the gap analysis on its own, and you end up scoring yourself against all 38 controls, including ones your risk profile never called for. Run the risk assessment on its own, and you pick treatments with no idea what already exists to deliver them. The methodology below interleaves the two. A clause-level gap review sets the scope and evidence base, the risk and impact assessments decide which controls are required, and a control-level gap review then scores only what matters. How AI-specific risks shape the methodology Traditional information security risk works from confidentiality, integrity, and availability. AI risk adds categories that don’t map neatly onto any of those: model drift, bias in training data, outputs nobody can explain, automation bias in the humans doing the reviewing, and dependence on third-party foundation models whose behavior changes without warning. ISO/IEC 23894, the companion guidance on AI risk management, adapts the ISO 31000 cycle (establish context, identify, analyze, evaluate, treat) to these sources rather than inventing a new one. That’s why the methodology here keeps the familiar ISO 31000 shape and changes the inputs, not the process. Regulatory and business drivers for a formal methodology The commercial driver is procurement. Enterprise security questionnaires now ask whether you ran an AI impact assessment, whether a human reviews high-stakes outputs, and which third-party models touch customer data. A documented methodology answers those questions with evidence instead of assurances. The regulatory driver is the EU AI Act, and its timeline moved in July. Regulation (EU) 2026/1744, the Digital Omnibus on AI, entered into force on July 27, 2026, and pushed the high-risk obligations for standalone Annex III systems from August 2, 2026 to December 2, 2027. Annex I embedded systems moved to August 2, 2028. The Article 50 transparency obligations still kicked in on August 2, 2026, as originally planned. Article 9 of the AI Act text on EUR-Lex requires a risk management system for high-risk AI that runs continuously across the system lifecycle, which is exactly what an ISO 42001 methodology gives you. Sixteen extra months is time to build it properly, not a reason to shelve it. Core Principles of an ISO 42001 Gap Analysis and Risk Assessment Methodology Four principles keep the methodology defensible in front of a certification body. Alignment with clauses 4 to 10 and Annex A. Every finding in the gap register cites a clause or an Annex A control identifier. Auditors work clause by clause, so a gap register organized any other way forces a translation step during the audit that nobody enjoys. Integration with the AI system impact assessment. Clause 6.1.4 is what separates ISO 42001 from every other Annex SL standard. The impact assessment looks outward at individuals, groups, and society. The risk assessment under 6.1.2 looks inward at the organization. The standard wants both as separate documented outputs, and the consequences you find in the impact assessment have to feed back into the risk assessment. So the methodology runs the impact assessment as a scheduled input to risk analysis, not something bolted on the week before the audit. Risk-based thinking applied to the AIMS itself. Clause 6.1.1 also asks you to consider risks and opportunities to the management system: someone leaving the AI governance function, a vendor retiring a model, a regulator changing its classification rules. These go in the same register with a different category tag. Defined inputs, outputs, and success criteria. Inputs are the AI system inventory, the scope statement, existing policies, data flow diagrams, model documentation, and your risk criteria. Outputs are the gap register, the AI risk register, impact assessment reports, the SoA, and the risk treatment plan. Success means each output traces to the others, every gap and risk has an owner, and an internal auditor could repeat the process and land somewhere similar. Insider Note: Impact assessments are where certification auditors probe hardest, because they’re the most distinctive part of ISO 42001 compared with ISO 27001. A recycled security risk register with “AI” pasted into the risk titles gets picked apart in Stage 2. Build the impact assessment methodology properly the first time. It’s far cheaper than rebuilding it under a nonconformity deadline. Preparing for the Gap Analysis and Risk Assessment Preparation is where most of the calendar time goes, and where most later problems start. Define scope, boundaries, and the AI system inventory. Scope under clause 4.3 has to name which AI systems, business units, and lifecycle stages the AIMS covers. You can’t write