Resistance to insecticides in the mosquito Anopheles gambiae s.l can jeopardize malaria vector control strategies. Previous studies have shown that the agricultural chemicals, used particularly for cotton protection, selected the insecticide resistant malaria vectors. Our study aimed at assessing the impact of three cotton pest management strategies in different ecological settings (conventional, organic and transgenic cotton growing areas) on the i) susceptibility to insecticides belonging to pyrethroids, DDT, carbamate and organophosphate tested on the main malaria vectors and ii) frequencies of kdr L1014F, during rainy season of 2008, 2009, 2013 and 2014 in Burkina Faso. From 2008 to 2014, most of populations of An. gambiae s.l from the three cotton growing areas exhibited a reduction in susceptibility to almost all insecticide classes. The frequency of kdr L1014F mutations varied depending on both localities and species within the An. gambiae complex, but no relationship was found between the cotton pest control strategies and the frequency of kdr L1014F. These results confirm the worrying status of insecticide multi-resistance within the vector mosquito species from Burkina Faso.