The proposed project focuses on the valorization of agro-industrial waste and effluents (manure and vinasse) for the production of bioenergy (biomethane) and a bioproduct that can be used for agronomic purposes or as a biofertilizer. The integrated treatment of agro-industrial waste has been previously tested in different projects developed under the research line “Biological Waste Treatment (TBR)” at the University of Cádiz (TEP-181 of the PAI), consisting of the application of the process in sequential thermophilic-mesophilic temperature phases. The codigestion of manure and vinasse can increase energy efficiency in this sector. Additionally, it offers operational and economic advantages (such as sharing treatment facilities, unifying management methodologies, and reducing investment and operating costs), and provides a solution to the environmental problem generated by this type of waste at the regional, national, and international levels. Furthermore, the proposed phased temperature process allows the final digested effluent to be classified as Class A biosolid according to the EPA (Title 40 Code of Federal Regulations Part 503 (40CFR 503)) for agronomic use, while promoting overall treatment in terms of volatile solids destruction, COD reduction, and pathogen inactivation (Salmonella and total and fecal coliforms). The main result of the project is to obtain an optimized protocol for the startup and operation of the sequential thermophilic-mesophilic anaerobic digestion process for the treatment of manure and vinasse from wine production. The project also aims for the rapid transfer of the technology to wineries and livestock farms that currently do not have an adequate treatment system.