In this study, the protein content and functional changes in soybeans cultured with Phellinus linteus HN00K9 were analyzed. P. linteus HN00K9 was cultured on soybeans. The crude protein content in soybeans cultured with HN00K9 (PMS) was 41.99%, which was higher than that in soybeans not cultured with the mushroom (UCS). The total free amino acid content in PMS increased to 39,963 mg/100 g, which was higher than that in UCS (36,817 mg/100 g). In particular, in PMS, glutamic acid accounted for 18.5% of the total amino acids at 7,413 mg/100 g. The total polyphenol content in PMS was 2.66 mg GAE/g, which was more than 45% higher than the amount in UCS (1.45 mg GAE/g). Additionally, PMS showed a DPPH radical scavenging activity of 33.3%, which was 3 times higher than that exhibited by UCS (11.5%), reflecting its high antioxidant content. Therefore, the PMS in this study has potential for use as a functional food material.