StarD7 is a member of the START protein family required for phosphatidylcholine delivery to the mitochondria, thus key to maintain mitochondrial structure. Its deficiency has been associated with an impairment of cellular processes, such as proliferation and migration, and it has also been reported that it is needed in myogenic differentiation. Here, we show that StarD7 deficiency in C2C12 muscle cells results in the accumulation of abnormal mitochondria, a reduced number of mitochondria per cell area and increased glycolysis. In addition, StarD7‐deficient cells undergo an increase in mitochondria‐ER contact sites, reduced connexin 43 expression, and disturbances in lipid handling, evidenced by lipid droplet accumulation and decreased levels in phosphatidylserine synthase 1 and 2 expression. Interestingly, StarD7‐deficient cells showed alterations in mitophagy markers. We observed accumulation of LC3B‐II and BNIP3 proteins in mitochondria‐enriched fractions and accumulation of autophagolysosomal and lysosomal vesicles in StarD7‐deficient cells. Furthermore, live‐cell imaging experiments of StarD7 knockdown cells expressing mitochondria‐targeted mKeima indicated an enhanced mitochondria delivery into lysosomes. Importantly, StarD7 reconstitution in StarD7‐deficient cells restores LC3B‐II expression in mitochondria‐enriched fractions at similar levels to those observed in control cells. Collectively, these findings suggest that StarD7‐deficient C2C12 myoblasts are associated with altered cristae structure, disturbances in neutral lipid accumulation, glucose metabolism, and increased mitophagy flux. The alterations mentioned above allow for the maintenance of mitochondrial function.