Intramyocellular lipid content (IMCL) serves as a good biomarker of skeletal muscle insulin resistance (IR). However, intracellular fatty acid metabolites [malonyl-CoA, long-chain acyl-CoA (LCACoA)] rather than IMCL are considered to be responsible for IR. This study aimed to investigate dynamics of IMCL and fatty acid metabolites during fed-to-starved-to-refed transition in lean and obese (IR) ZDF rats in different muscle-types: soleus (oxidative), extensor digitorum longus (EDL, intermediary), and white tibialis anterior (wTA, glycolytic). In the fed state IMCL were significantly elevated in obese compared to lean rats in all three muscle-types (soleus: 304%, EDL: 333%, wTA: 394%) in the presence of elevated serum triglycerides, but similar levels of free fatty acids (FFA), malonyl-CoA and total LCACoAs. During starvation, IMCL in soleus remained relatively constant, while in both rat groups IMCL increased significantly in wTA and EDL following comparable dynamics of starvation-induced FFA availability. The decreases of malonyl-CoA in wTA and EDL during starvation were more pronounced in lean than in obese rats, while there were no changes in soleus muscles for both groups. The concomitant increase in IMCL with the fall of malonyl-CoA support the concept that, as a reaction to starvation-induced FFA availability, muscle will activate lipid oxidation the more the lower its oxidative capacity and, then, store the rest as IMCL.