Thermal selective reactions were studied on oxothieno[2,3-d]pyrimidine-6-carboxamide 3 with POCl3 and PCl5. At 25-50 °C, the C7-amide rearranges to nitrile furnished compound 4 in 85-90% yield, while at 80-110 °C furnished mixture of products 4 and 5 in 28-68% yields. The chloro displacement with amines in compound 5 yielded 4-aminothieno[2,3-d]pyrimidine-6-carbonitrile derivatives 8(a-h) and 9(a-e). Antimicrobial activity of new compounds was studied against several bacteria such as Staphylococcus aureus MTCC-96, Escherichia coli MTCC-443, Pseudomonas aeruginosa MTCC-4 41, Streptococcus pyogenes MTCC-442 and fungi Aspergillus niger MTCC-282, Aspergillus clavatus MTCC-1323, Candida albicans MTCC-227 using broth microdilution method. Compounds 4, 8b, 8d, 8e, 8h and 9a showed promising antibacterial activity compared to ampicillin and compounds 8b, 8h showed better antifungal activity compared to greseofulvin.