With the aim of developing a general and practical method for library production, a novel and efficient two-phase microwave-assisted cascade reaction between isatins and β-ketoamides in [Bmim]BF4/toluene was developed for the synthesis of pyrrolo[3,4-c]quinoline-1,3-diones. The features of this methodology are, the use of microwave-assisted rapid synthesis, mild reaction conditions, high yields, operational simplicity, facile product separation, and recyclability. Furthermore, the antibacterial activities of the pyrrolo[3,4-c]quinoline-1,3-dione derivatives produced were evaluated against Gram-negative bacteria (Escherichia coli, Pseudomonas aeruginosa, and Enterobacter aerogenes) and Gram-positive bacteria (Bacillus cereus and Staphylococcus aureus). These derivatives showed antibacterial activities against Gram-positive strains that were at least equivalent to that against Gram-negative strains. Compound 7{3,5} displayed the most potent antibacterial activity against P. aeruginosa (MIC = 0.5 μg/mL) and greater activity than standard ampicillin (MIC = 1 μg/mL). Compound 7{4,7} exhibited the best inhibitory activity against E. coli and E. aerogenes (MIC = 1 and 0.5 μg/mL), compared with the standard ampicillin (both MICs = 1 μg/mL). The synthesized pyrrolo[3,4-c]quinoline-1,3-diones are expected to be widely used as lead compounds for the development of new antibacterial agents.