Animal mortalities management is a challenging and ecologically concerning issue in Agro-Silvo-Pastoral systems. Conventional methods used are not environmentally friendly, are likely to disperse disease to human and animals and do not promote the circularity of livestock units. The absence of national and European legal frameworks further compounds the problem, largely due to pathogen concerns. Composting animal mortalities as an innovative solution in Europe can address these challenges by safeguarding natural resources, reducing pollution, and enhancing soil organic carbon and nutrient recycling. This study proposes a composting methodology for managing animal mortalities and green wastes (prunings), offering significant benefits to Agro-Silvo-Pastoral systems. Two composts were prepared using sheep mortalities and green wastes (GWs). Clinoptilolite (natural zeolite) was added to one of the two composts to improve the properties of the final product. Comparing compost properties with EU standards for safe compost use as soil amendments indicates that the zeolite-compost can be freely utilized for plant growth, land rehabilitation, and carbon sequestration without any limitation. The research findings demonstrate advantages for Agro-Silvo-Pastoral systems, including improved mortalities management, enhanced soil properties, and increased soil organic matter content.