Cordyceps militaris, well known for its therapeutic potential in managing type-2 diabetes through the inhibition of α-amylase and α-glucosidase enzymes, was the central focus of this research, which investigated the influence of various cultivation substrates on its enzymatic inhibitory properties and bioactive compound content. Previous studies have primarily focused on the general pharmacological benefits of C. militaris but have not thoroughly explored how different substrates affect its bioactive profile and enzyme inhibitory activities. This study aimed to evaluate the impact of substrate selection on the enzyme inhibition activities and the levels of bioactive compounds such as cordycepin and adenosine in C. militaris, demonstrating that substrate selection markedly affects both these enzymes’ inhibition activities and bioactive compound levels. Particularly, C. militaris fruiting bodies grown on Brihaspa atrostigmella showed the highest concentrations of cordycepin (2.932 mg/g) and adenosine (1.062 mg/g). This substrate also exhibited the most potent α-glucosidase inhibition with an IC50 value of 336.4 ± 16.0 µg/mL and the most effective α-amylase inhibition with an IC50 value of 504.6 ± 4.2 µg/mL. Conversely, C. militaris cultivated on the solid residues of Gryllus bimaculatus displayed the strongest xanthine oxidase (XOD) inhibition, with the lowest IC50 value of 415.7 ± 11.2 µg/mL. These findings highlight the critical role of substrate choice in enhancing the medicinal properties of C. militaris, suggesting that optimized cultivation can enhance the bioactive properties for more effective natural therapies for diabetes and other metabolic disorders. This study not only extends the understanding of C. militaris’ pharmacological potential but also illustrates its applicability in developing customized treatment options.