6-Prenylapigenin (1) and 8-prenylapegenin (2) were semi-synthesized from apigenin by nuclear prenylation. Morusin (3) was isolated from the root bark of Morus alba L. The microbial transformation studies of these three bioactive prenylated apigenin derivatives were performed using eighteen cell cultures in order to select microorganisms capable of transforming them. It was identified that Mucor hiemalis (KCTC 26779) showed the ability to metabolize the parent compounds (1–3) into three new (4–6) and one known (7) glucosylated derivatives with high efficiency. Their structures were established as 6-prenylapigenin 7-O-β-d-glucopyranoside (4), 8-prenylapigenin 7-O-β-d-glucopyranoside (5), morusin 5-O-β-d-glucopyranoside (6), and morusin 4′-O-β-d-glucopyranoside (7) by the spectroscopic methods.