Anaerobic co-digestion (AcoD) is a mature and consolidated waste management technology that can transform agro-industrial by-products into biogas and digestate. This study conducted a techno-economic assessment of bioenergy and agricultural fertilizer production from AcoD of sewage sludge, wine vinasse, and poultry manure. In this case study, three configurations were investigated: i) Scenario 1, AcoD in thermophilic temperature; ii) Scenario 2, AcoD in mesophilic temperature; and iii) Scenario 3, AcoD in a temperature phase (TPAD) system, where the digestate produced in the first reactor (thermophilic) feeds the second reactor (mesophilic). The process was designed to manage 24,022 m3 wine vinasse y-1, 24,022 m3 sewage sludge y-1, and 480 m3 poultry manure y-1. The major cost was the fixed capital investment for the single-stage (320,981 USD) and TPAD processes (379,698 USD). The TPAD process produced the highest electricity (1058.99 MWh y-1) and heat (4765.47 GJ y-1) with the lowest cost of manufacturing for electricity (84.99 USD MWh-1), heat (0.019 USD MJ-1), and fertilizer (30.91 USD t-1). Regarding the profitability indicators, the highest net present value (509,011 USD) and the lowest payback time (4.24 y) were achieved for Scenario 3. In conclusion, TPAD is a profitable and sustainable waste-to-energy management technology that can be applied in a circular economy framework to recover bioenergy and fertilizer, contributing to decreasing the carbon footprint of the agri-food sector.