Resistance to insecticides in the mosquito Anopheles gambiae s.l can jeopardize malaria vector control strategies in Africa. Previous studies have shown that the agricultural use of pesticides, particularly for cotton protection, contributes to the selection of insecticide resistance of malaria vector mosquitoes. Our study aimed at assessing the impact of three cotton pests control strategies in different ecological settings (conventional, organic and transgenic cotton growing areas) on the i) susceptibility to insecticides (Permethrin and Deltamethrin (pyrethroids), DDT (organochlorine), Bendiocarb (carbamate), chlorpyriphos-methyl (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, West Africa. From 2008 to 2014, a reduction in susceptibility to all insecticides except chlorpyriphos-methyl was detected in most populations of An. gambiae s.l from the three cotton growing areas. The frequency of kdr-w mutations varied depending on localities and species within the An. gambiae complex, but we found no relationship between the cotton pest control strategy and the frequency of kdr-w or, otherwise with phenotypic resistance evaluated from bioassays. The implementation of organic cotton and Bt transgenic cotton programs in certain areas of Burkina Faso does not change the insecticide resistance status of An. gambiae s.l. populations in the region concerned. These results confirm the worrying status of insecticide multi-resistance of the main malaria vector mosquito species in Burkina Faso.