Solanine (SOL), chaconine (CHA), and tomatine (TOM) are plant secondary metabolites produced mainly by the species of Solanaceae family, such as tomato Solanum lycopersicum L. These glycoalkaloids (GAs) have a wide range of biological activity, also in insects. However, their mechanisms of action are not precisely understood. The purpose of the study was to investigate how pure GAs and tomato leaf extract (EXT) affect glycolysis, Krebs cycle and β-oxidation of fatty acid pathways in Tenebrio molitor L. beetle. For this purpose, the larvae were injected with SOL, CHA, TOM, and EXT at two concentrations (10–8 and 10–5 M). For experiments, fat body, gut, and heamolymph samples were collected 2 and 24 h after injection. Then, the changes in the expression level of phosphofructokinase, citrate synthase, and β-hydroxyacyl-CoA dehydrogenase were measured using the RT-qPCR technique. The catalytic activity of these enzymes and the carbohydrate level in insects after GA treatment were determined by spectrophotometric method. Furthermore, the analysis of the amount of amino acids in tissues was performed with a GC–MS technique. The results obtained show that the GAs changed the activity and expression of the genes encoding key enzymes of crucial metabolic pathways. The effect depends on the type of GA compound, the tissue tested, and the incubation time after treatment. Furthermore, TOM and EXT affected trehalose concentration in the insect hemolymph and led to accumulation of amino acids in the fat body. The observed changes may indicate a protein degradation and/or enhanced catabolism reactions for the production of ATP used in detoxification processes. These results suggest that GAs alter energy metabolism in the mealworm T. molitor. The study contributes to our understanding of the mechanisms of action of secondary metabolites of plants in insects. This knowledge may allow the design of new natural biopesticides against insect pests because proper energy metabolism is necessary for the survival of the organism.