Background: To curb the emergence of antibiotic-resistant Mycobacterium leprae strains, the WHO recommends monitoring of antimicrobial resistance (AMR). In Madagascar, molecular surveillance of resistance to anti-M. leprae drugs, remains limited geographically and in terms of quantitative data. A clinical trial on leprosy prophylaxis (PEOPLE) conducted in the district of Miandrivazo provided an opportunity to explore the feasibility of an integrated approach for improving leprosy surveillance and resistance monitoring in Madagascar. This study aimed to i) determine the genetic diversity of the identified M. leprae strains, (ii) detect mutations associated with AMR, (iii) evaluate and compare the acceptance rate of low-invasive sampling methods with that of skin biopsies, and (iv) assess seropositivity for anti-M. leprae PGL-I IgM. Methods: Patients were identified through door-to-door screening and skin biopsies (SB), fingerstick blood (FSB) and nasal swabs (NS) were collected. SB were analyzed by RLEP qPCR for detection of M. leprae DNA, resistance testing using LiPA (Line Probe Assay), and resistance analysis and SNP and/or VNTR genotyping using Sanger sequencing and Deeplex Myc-Lep. NS and FSB samples were used to detect bacterial colonization by RLEP qPCR and detect past and/or present infection by measuring anti-M. leprae PGL-I IgM levels. Results: 80 leprosy patients were identified, including 41 multibacillary and 39 paucibacillary. Out of these, 57 accepted NS, 47 FSB, and 33 SB. High levels of anti-PGL-I IgM were detected in 6/47 FSB samples. RLEP qPCR was positive in 4/57 NS samples and 28/33 SB samples. Among SB positive, 12 yielded interpretable results when combining data from LiPA, Deeplex Myc-Lep, and Sanger sequencing. No drug resistance conferring mutations were detected. All strains belonged to the 1D-Malagasy genotype, and VNTR analysis for 7 samples with results available across 9 loci showed 7 unique types, with loci GAA21, GTA9, and AC8a were the most informative for strain differentiation. Conclusion: Despite the small sample size, this study shows that NS and FSB samples are well accepted in patients. No mutations conferring resistance were identified and the M. leprae strains belong to the 1D-Malagasy genotype. These findings support the feasibility of field-based molecular surveillance and provide a foundation for expanding AMR monitoring in Madagascar.