Phellinus linteus is a famous medicinal mushroom which exhibits various biological activities. This study aimed to investigate the effects of solid-state fermentation by Ph. linteus on the yield of bioactive compounds and antioxidant activities of beans. Four bean substrates were prepared and inoculated with inoculum of three strains of Ph. linteus, respectively. During the cultivation, the harvested samples were dried, grounded, extracted, and determined the contents of bioactive compounds and antioxidant activities. The results indicated that the mung bean fermented by Ph. linteus 04 had the highest polysaccharide content (98.8 mg/g). The highest total phenolic and flavonoid contents were in fermented soybeans by Ph. linteus 03 (15.03 mg gallic acid equivalents/g and 63.24 mg rutin equivalents/g, respectively). The 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) radical scavenging activities of hot water extracts were higher than those of ethanolic extracts for fermented beans by three Ph. linteus strains. However, the superoxide anion radical scavenging ability of ethanolic extracts was higher than those of hot water extracts in the fermented beans of the three strains. The ferrous ion (Fe2+)-chelating abilities of hot water extracts were higher than those of ethanolic extracts in fermented beans by Ph. linteus 03 and 04. In contrast, ethanolic extracts were higher than hot water extracts in fermented beans by Ph. linteus 06. Overall, these results indicate that the fermentation by Ph. linteus strains increased the bioactive compounds and antioxidant activities of four beans.