This study shows that (i) habitual PA is lower in T1D and T2D within the first year after diagnosis, (ii) increases in habitual PA over 5 years do not associate with improvements of insulin sensitivity in 36% of individuals with T2D, (iii) rs540467 SNP of the NDUFB6 gene is associated with PA-mediated changes in insulin sensitivity, body composition and liver fat estimates (iv) silencing NDUFB6 in myotubes lowers mitochondrial respiration and inhibits the contraction-mediated rescue from palmitate-induced insulin resistance. This evidence concerns the gene NDUFB6 and type 2 diabetes mellitus.