Abstract Background Coverage is an important indicator to assess both the performance and effectiveness of public health programs. Recommended methods for coverage estimation for the treatment of severe acute malnutrition (SAM) can involve active and adaptive case finding (AACF), an informant-driven sampling procedure, for the identification of cases. However, as this procedure can yield a non-representative sample, exhaustive or near exhaustive case identification is needed for valid coverage estimation with AACF. Important uncertainty remains as to whether an adequate level of exhaustivity for valid coverage estimation can be ensured by AACF. Methods We assessed the sensitivity of AACF and a census method using a capture-recapture design in northwestern Nigeria. Program coverage was estimated for each case finding procedure. Results The sensitivity of AACF was 69.5% (95% CI: 59.8, 79.2) and 91.9% (95% CI: 85.1, 98.8) with census case finding. Program coverage was estimated to be 40.3% (95% CI 28.6, 52.0) using AACF, compared to 34.9% (95% CI 24.7, 45.2) using the census. Depending on the distribution of coverage among missed cases, AACF sensitivity of at least ≥70% was generally required for coverage estimation to remain within ±10% of the census estimate. Conclusion Given the impact incomplete case finding and low sensitivity can have on coverage estimation in potentially non-representative samples, adequate attention and resources should be committed to ensure exhaustive or near exhaustive case finding. Trial registration ClinicalTrials.gov ID NCT03140904. Registered on May 3, 2017.