AbstractDigitally controlled reactors can optimize biological reactions and process control through a neural network system. This study reports on the design, fabrication, and automation of a laboratory‐scale anaerobic reactor for the management of agrifood byproducts and bioenergy recovery. The process described here can digitally control the operational parameters, which is beneficial for stable methane production. The proposed process comprises the digital measurement of temperature, pH, humidity, biogas volume, and methane composition by integrating the data in a processor module. The proposed automated reactor can assist significantly in controlling and monitoring the anaerobic digestion process, providing decision making during waste management and bioenergy recovery. A case study is described with the application of automated reactors in a pilot‐scale plant, operated with the flow of 8 m3 slaughterhouse wastewater per day and a biogas production of 10 m3 h−1. The automated pilot‐scale process presents many advantages, including a continuous mode of operation and a faster adaptation of the microorganisms to the substrate, improving biogas production.