In circular bioeconomy, biowaste has a great potential for utilization as organic fertilizer. This study aims to evaluate the probability of anaerobically digested biowaste to qualify as organic fertilizer, within the framework of the EU fertilizer Regulation. The parameters investigated are the heavy metal and nutrient content of the solid and liquid fertilizers, and soil improvers. Two collection systems for the organic fraction of municipal solid waste (OFMSW) are assessed, i.e., source-separation (SS) and mechanical separation (MS) from unsorted waste. A modelling tool is developed for calculating the quality of the digestate, purposed as organic fertilizer, based on feedstock data. Four scenarios of biogas production efficiencies are modelled (60%, 70%, 80%, and 90% of volatile solids removal) to cover the different anaerobic digestion configurations. A Monte Carlo simulation is applied to estimate the probability of exceeding the regulatory limits for heavy metal concentration in organic fertilizers. The statistical analysis of the biowaste illustrates that the quality of the SS-OFMSW is higher than the MS-OFMSW. The Monte Carlo simulation shows that the SS-OFMSW digestate has 18% probability of exceeding the regulatory limit value for Cadmium and less than 10% for the rest of the heavy metals. The MS-OFMSW digestate illustrates a higher risk that ranges from 11% to 51%. The study justifies the explicit exclusion of the MS-OFMSW from the positive list of inputs for the production of organic fertilizers in the circular economy market. High quality organic fertilizers can contribute to closing the nutrient loop by returning them on agricultural soil while safeguarding soil health and food safety.