Nowadays, municipal solid waste (MSW) management is one of the most critical issues. MSW may threaten the environment; however, the concerning high organic fraction content can be useful. This study aimed to compare the suitability of mechanically sorted organic fraction (OF) of MSW and source-segregated biowaste for biofertilizer usage. The compost and the effluents compositions were analyzed. Compost derived from biowaste can be applied to the soil, while, after processing OFMSW, the metal contents are too high. The exceeding limit values were noted, e.g., lead (over 80 mg/kg) and chrome (75 mg/kg). Effluents from biowaste treatment fulfill the national and UE fertilizers’ requirements, considering the heavy metal contents, while effluents from OFMSW treatments exceed the limit values. The biggest exceedings were observed for nickel (over 3 mg/kg) and zinc (over 500 mg/kg). In general, the heavy metal contamination of byproducts from the OFMSW treatment was much higher. At the same time, the biogenic elements, e.g., nitrogen and phosphorus concentrations, were much lower than the biowaste treatment byproducts; however, even for them, the concentrations of the biogenic elements were too low to meet EU requirements. The compost and effluents derived from the biowaste treatment may be suitable for crop applications, considering the current national requirements.