A three-step method for obtaining pyrrolo[1,2-a]pyrazine-4,7-dicarboxylates was presented. The method involves the N-alkylation of 5-formylpyrrole-3-carboxylates with bromoacetate, followed by the aminoalkenylation of the N-alkoxycarbonylmethyl group using dimethylformamide di-tert-butyl acetal, and further annulation of the pyrazine ring in the presence of ammonium acetate. Procedures for selective hydrolysis, halogenation, arylation, and alkynylation of the synthesized dicarboxylates were described. The in silico evaluation of the potential bioactivity of the synthesized dicarboxylates 4a–f, dicarboxylic acids 7a–c,e, halogenated dicarboxylates 8f–j, and dicarboxylic acids 10a–e was carried out. As seen from the screening of antimicrobial activity, the synthesized compounds 7a–e, 8c,f–j, 10a–e exhibit inhibitory and bactericidal activity against several bacteria and fungi. The highest activity against Klebsiella pneumonia, Staphylococcus aureus, and Bacillus subtilis has been established for the compound 8f with a MIC of 15.625 µg/mL, and the highest antifungal activity against Candida albicans was found for the compounds 8f, 8g, and 8i (МІС=15.625 µg/mL). The molecular docking data show that the compound 8i has the highest affinity to the ThiM Klebsiella pneumoniae kinase, and compounds 8i, 8j are noted for their highest affinity to the DNA gyrase from Staphylococcus aureus.