In the search for new therapeutic agents against microbial infections, two novel series of monocyclic and tricyclic 5-(phenylazo)thiophene systems were synthesized based on 3-amino-2-thioxopyrimidinone and 2-cyanoacetamidothiophene derivatives 4 and 6. Functionalization of the pyrimidine ring in precursor 4 resulted in the formation of the target tricyclic condensed thiophenes 7, 12, and 13a, b, by the application of a variety of addition, substitution, and condensation reactions. On the other hand, derivatization of the versatile cyanoacetylated compound 6 led to a second series of monocyclic N-substituted aminothiophenes 15, 17, 19, and 20, through convenient methods. The new thiophene-based derivatives were tested for their antimicrobial activity with reference to relevant standard drugs. They displayed different levels of antibacterial activity, with compound 7 showing essentially the highest antipseudomonal activity. As for antifungal action, the compounds under investigation, unfortunately, had no inhibitory effects against test fungi isolates except for 7 and 20, that revealed slight inhibition.