Simple and green synthetic procedures constitute an important goal in organic synthesis. The combination of multicomponent reactions (MCRs) and unconventional solvents has become a new research direction, which enables simultaneous growth of both MCRs and green solvents toward ideal organic synthesis. In this paper, we have summarized recent results of MCRs obtained in unconventional media using water and β-cyclodextrin, as supramolecular catalyst, for the synthesis of pyrano[2,3-d]-pyrimidinone (4a–q) derivatives. The compounds were evaluated for their in vitro antimicrobial activity. Among the synthesized compounds, compounds 4h, 4m and 4p exhibited higher antimicrobial activity than ciprofloxacin used as the reference drug. Most of the synthesized compounds have good to excellent antimicrobial activity. Furthermore, \ molecular docking study was performed to help understand binding interactions of the most active analogs with C30 carotenoid dehydrosqualene synthase enzyme.