The study objective was to adjust the hydrodynamic disintegrator dedicated to sewage sludge pre-treatment (HDS) to work with agricultural substrate. This involved the development and implementation of a mathematical model of flow via the device’s domain. An innovative disintegrator (HAD—hydrodynamic disintegrator for agriculture) was designed, built, and tested based on the obtained results. The main improvements to the HDS include the implementation of shredding knives in order to overcome clogging by crushed substrate, and the application of ribs in the recirculation zone, contributing to the development of an additional structure damage zone. The challenge of this study was also to determine the operating parameters of the HDA that would provide for an increase in methane production with positive energy balance. The testing procedures, for which maize silage was selected, involved batch disintegration tests and biochemical methane potential tests. No clogging of rotor or spontaneous shutting off of the device, in other words, problems that had occurred in the HDS, were observed. The applied pre-treatment method permitted an increase in the methane potential of maize silage by 34.4%, 27.0%, and 21.6%, respectively for samples disintegrated at energy densities of 10 kJ/L, 20 kJ/L, and 35 kJ/L with net energy profit.