Azole antifungal agents are widely used as active ingredients in antifungal pharmaceuticals and agricultural fungicides. An increase in the use of azole antifungals has resulted in an increase in the concentration of these compounds in wastewater and surface water, with potential implications for agriculture. In the present study, bifonazole (BIF) and clotrimazole (CTZ) were selected for investigation because of their widespread use in topical formulations and persistence in the environment. The mycoremediation capacity of BIF and CTZ by mycelia of Lentinula edodes in in vitro culture was evaluated. The main aim of this study was to identify the presumable biodegradation products of the investigated active pharmaceutical substances using the LC/MS/MS method. For this purpose, the media were enriched with the following active pharmaceutical ingredients selected for this study: BIF powder, CTZ powder, and BIF cream, each of them at the same concentration of 0.1 mg/mL. Subsequently, thin-layer chromatography coupled with densitometry was used to evaluate the content of BIF and CTZ in mycelium from in vitro cultures of L. edodes. The degradation process was found to affect primarily the imidazole moiety of both investigated compounds. In addition, the amounts of undegraded investigated compounds were found to be 4.98, 9.26, and 4.56 mg/g dry weight for BIF powder, CTZ powder, and BIF cream, respectively. Therefore, the findings of this study revealed that L. edodes could be considered for remediation of pollution caused by azole antifungal agents.