Acute myeloid leukaemia (AML) is a haematologic malignancy with high relapse incidence and mortality. Approximately one‐third of AML patients carry an fms‐like tyrosine kinase 3 (FLT3) mutation, often associated with GLI expression and Hedgehog signalling. AML cells shape their microenvironment into a leukaemia‐permissive space by releasing extracellular vesicles (EVs). EVs can transfer chemoresistance and thereby play an important role in refractory and relapsing diseases. Here, we discovered a synergistic effect of combined treatment with the FLT3 inhibitor Crenolanib and the Hedgehog pathway inhibitor HPI‐1 in the AML cell lines MOLM‐14 and MV4‐11. By comparing cellular and EV proteomes, we found that transport of ribosomal proteins, such as RPS26 and RPL27A, and ErbB pathway members such as GAB1, GRB2 and SHC1 to EVs, is selectively avoided upon treatment with Crenolanib. These findings were corroborated by comparative proteomics of EVs derived from AML patients and healthy donors.