The World Health Organization (WHO)’s 2030 NTD Road map advocates for greater domestic ownership, mainstreaming, and integration of NTD programs, which in turn requires more capacity strengthening in the short term. This guide addresses one critical gap of the availability of resources to support the use of qualitative methods to strengthen MDA through a six step process. It aims to facilitate adaptive program learning for MDA by providing guidance on qualitative study design, implementation, analysis, and prioritization of recommendations, while also triangulating findings with existing knowledge. The main document takes the reader through the six steps and contains links to the relevant annexes for each step of the process. Annexes 1-8 can be accessed by clicking on the following links: Annex 1, Annex 2, Annex 3, Annex 4, Annex 5, Annex 6, Annex 7, Annex 8.