Here, we detail our optimized protocol for the identification of drug targets in Leishmania donovani using thermal proteome profiling. This approach is based on the principle that binding of a drug to its protein target can significantly alter the thermal stability of that protein. By monitoring changes in the thermal stability of proteins within drug-treated and untreated cell lysates, using mass spectrometry combined with tandem mass tag labeling, putative targets of the drug can be identified in an unbiased manner. For further details on the use and application of this protocol, please refer to Paradela et al. (2021).