Insulin deprivation in type 1 diabetes (T1D) individuals increases lipolysis and plasma free fatty acids (FFA) concentration, which can stimulate synthesis of intramyocellular bioactive lipids, such as ceramides (Cer) and long chain fatty acid-CoAs (LCFa-CoAs). Ceramide was shown to decrease muscle insulin sensitivity and at mitochondrial level stimulates reactive oxygen species production. Here we show that insulin deprivation in streptozotocin diabetic C57BL/6 mice increases quadriceps muscle Cer content, which was correlated with concomitant decrease in the body fat and increased plasma FFA, glycosylated hemoglobin level (%A1C) and muscular LCFa-CoA content. The alternations were accompanied by increase in proteins expression in LCFa-CoA and Cer synthesis (FATP1/ACSVL5, CerS1, CerS5), decrease in the expression of genes implicated in muscle insulin sensitivity (GLUT4, GYS1) and inhibition of insulin signaling cascade by AKTα and GYS3β phosphorylation under acute insulin stimulation. Both the content and composition of sarcoplasmic fraction sphingolipids were most affected by insulin deprivation, whereas mitochondrial fraction sphingolipids remained stable. The observed effects of insulin deprivation were reversed except for content and composition of LCFa-CoA, CerS protein expression, GYS1 gene expression and phosphorylation status of AKT and GYS3β when exogenous insulin was provided by subcutaneous insulin implants. Principal component analysis and Pearson's correlation analysis revealed close relationships between the features of the diabetic phenotype, the content of LCFa-CoA's and Cer's containing C18-fatty acids in sarcoplasm, but not in mitochondria. Insulin replacement did not completely rescue the phenotype, especially regarding the content of LCFa-CoA, and proteins implicated in Cer synthesis and muscle insulin sensitivity.