Cannabinoids are chemical substances present in the cannabis plant, which are recognized for their capability to be involved in the endocannabinoid system in humans and animals, hence raised concerns. More than a hundred different cannabinoids have been identified within the plant such as cannabidiol (CBD) and tetrahydrocannabinol (THC). Where cannabis is legally and widely used, such as areas with medical or recreational cannabis programs, various cannabinoids are found in concentrations from ng/L to μg/L in wastewater influent. These compounds are considered emerging contaminants, highlighting the need for research into treatment methods to efficiently eliminate them from the effluent of wastewater treatment plants before their release into natural water systems. In this study, the feasibility of soybean peroxidase catalyzed—as an eco-friendly alternative—removal of selected compounds from synthetic wastewater was monitored using high performance liquid chromatography, including optimization of the most important operational conditions, hydrogen peroxide concentration, pH, and enzyme activity. 2-Methylresorcinol, as a model compound, and CBD were found to be substrates for the enzyme, having about 100% removal efficiency at pH 7 and 8, respectively. A time-course study was determined under the optimized reaction conditions. The results support the possibility of soybean peroxidase-catalyzed treatment of the cannabinoids of emerging concern.