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The present work evaluated the effect of microwave roasting on total polyphenol content (TPC), total flavonoid content (TFC), 2,2-diphenyl-1-picrylhyrazyl (DPPH) radical scavenging activity, some selected compounds, and the mineral content of coffee beans. Coffee bean powder was roasted at three microwave power levels (450, 720, and 900 W) and treatment durations (4, 6, and 8 min). The TPC, TFC, and DPPH radical scavenging activity were increased by increasing the microwave power and roasting duration, but detrimental effects were observed at higher power levels and longer treatment durations. The highest TPC, TFC, and DPPH radical scavenging activity were detected for the sample treated at 720 W for 6 min. The mineral content was only increased in the sample treated at 450 W for 4 min; all other treatments decreased the mineral content. Microwave power levels and treatment durations showed a significant increase in the browning intensity of the coffee bean extract. The selected coffee bean compounds as analysed by GC-MS were affected in different ways by microwave treatment. The relative percentage of caffeine was increased from 40.06 to 49.12% when treated at 450 W for 4 min, while n-hexadecanoic acid content was decreased from 33.86% in untreated coffee beans to 16.31% when treated at 450 W for 4 min. There was also the formation of new compounds such as octadecanoic acid-methyl ester, vitamin E, and stigmasterol upon microwave roasting of coffee beans. Based on the above results, microwave heating can be used as a roasting method for coffee beans.