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The objective of the current study was to investigate the role of the MDH enzyme system in liver cells of alloxan-induced diabetic rats and to examine how the administration of inulin from Jerusalem artichoke affects the enzyme’s activity and gene transcription in these diabetic rats’ livers. In this study, male Wistar rats weighing 150-200 g were selected for the experiment. Diabetes mellitus was induced by a single intraperitoneal injection of 5% alloxan monohydrate (in 0.9% saline). The control group received an equivalent amount of saline solution. Statistical analysis was performed using StatTech v. 1.2.0 software. An increase in NAD-dependent malate dehydrogenase (MDH) activity, accompanied by the emergence of a novel liver isoform, was observed in rats with alloxan-induced diabetes. This finding suggests the potential involvement of the malate dehydrogenase enzyme system in the body’s adaptive response to oxidative stress induced by biochemical changes in diabetic cells. In type I diabetes, this rise in enzyme activity is associated with the appearance of an additional MDH isoform in peroxisomes. Gene expression analysis of mdh1 and mdh2 indicates that diabetes triggers enzyme activation at the gene transcription level. When inulin was administered, it significantly reduced blood glucose levels in rats with alloxan-induced diabetes and restored the regular transcriptional activity of these genes. Consequently, the formation of the new MDH isoform was prevented. This suggests that inulin could be a promising option for pharmacologically managing the metabolic changes associated with diabetes-related pathologies.