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Abstract Introduction Measuring the coverage of HIV prevention services for key populations (KPs) has consistently been a challenge for national HIV programmes. The current frameworks and measurement methods lack emphasis on effective coverage, occur infrequently, lack timeliness and limit the participation of KPs. The Effective Programme Coverage framework, which utilizes a programme science approach, provides an opportunity to assess gaps in various coverage domains and explore the underlying reasons for these gaps, in order to develop targeted solutions. We have demonstrated the application of this framework in partnership with the KP community in Nairobi, Kenya, using an expanded Polling Booth Survey (ePBS) method. Methods Data were collected between April and May 2023 among female sex workers (FSWs) and men who have sex with men (MSM) using (a) PBS, (b) bio‐behavioural survey and (c) focus group discussions. Data collection and analysis involved both KP community and non‐community researchers. Descriptive analysis was performed, and proportions were used to assess the programme coverage gaps. The data were weighted to account for the sampling design and unequal selection probabilities. Thematic analysis was conducted on the qualitative data. Results The condom programme for FSW and MSM had low availability (60.2% and 50.9%), contact (68.8% and 65.9%) and utilization (52.1% and 43.9%) coverages. The pre‐exposure prophylaxis (PrEP) programme had very low utilization coverage for FSW and MSM (4.4% and 2.8%), while antiretroviral therapy utilization coverage was higher (86.6% and 87.7%). Reasons for coverage gaps included a low peer educator‐to‐peer ratio, longer distance to the clinics, shortage of free condoms supplied by the government, experienced and anticipated side effects related to PrEP, and stigma and discrimination experienced in the facilities. Conclusions The Effective Programme Coverage framework allows programmes to assess coverage gaps and develop solutions and a research agenda targeted at specific domains of coverage with large gaps. The ePBS method works well in collecting data to understand coverage gaps rapidly and allows for the engagement of the KP community.