In Sub-Saharan Africa, An. gambiae sensu lato (s.l.) Giles 190, largely contributes to malaria transmission. Therefore, the authors carry out a proteomic analysis to compare its metabolic state, depending on different pesticide pressures by selecting areas with/without cotton crops. The proteomes data are available via ProteomeXchange with identifier PXD016300. From a total of 1.182 identified proteins, 648 are retained for further statistical analysis and are attributed to biological functions, the most important of which being energy metabolism (120 proteins) followed by translation-biogenesis (74), cytoskeleton (71), stress response (62), biosynthetic process (60), signalling (44), cellular respiration (38), cell redox homeostasis (25), DNA processing (17), pheromone binding (10), protein folding (9), RNA processing (9), other proteins (26) and unknown functions (83). In the Sudano-Sahelian region, 421 (91.3%) proteins are found in samples from areas both with and without cotton crops. By contrast, in the Sahelian region, only 271 (55.0%) are common to both crop areas, and 233 proteins are up-regulated from the cotton area. The focus is placed on proteins with putative roles in insecticide resistance, according to literature. This study provides the first whole-body proteomic characterisation of An. gambiae s.l. in Burkina Faso, as a framework to strengthen vector control strategies.