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Mechanical composting is a popular treatment method for the mechanically separated organic fraction of municipal solid wastes to stabilize the waste material and reduce its environmental impacts. The model and life cycle inventory database are created based on the existing centralized mechanical composting facility located in Chania (Crete, Greece). This study aims to assess all stages of the composting process, wherein input-output flows are comprehensively analyzed based on specific waste fragments. The transfer coefficients are calculated for each waste fragment throughout the processes. The degradation rate is measured as kg of C and N released per Mg of the treated material. The results show that process degradation rates are independent of the initial fragmental composition. This is the first study that accurately models the fate of distinctive waste fragments in a composting plant, while the developed life cycle inventory (with regard to mass and energy balances) can be applied to estimate the environmental impacts regarding mechanical composting the organic fraction of municipal solid wastes.