It has been proven that the biocenosis of microalgae and bacteria improves the chemical properties of biomass for its use in anaerobic digestion. However, this anaerobic digestion can be limited by the strong, compact, and complex structure of granulated biomass. Therefore, there is a need to search for an effective method for microalgal–bacterial granular sludge pretreatment, which has not been undertaken in previous scientific works. In this study, ultrasonic pretreatment was used to determine the effects of sonication on anaerobic digestion efficiency. Anaerobic digestion was performed in batch respirometric reactors. It was found that the ultrasonic pretreatment enhanced the biomass solubility; thus, the organic matter concentration increased more than six times compared to the variant without pretreatment. The study showed a positive effect of sonication on the kinetics of the anaerobic process and methane production. The highest methane yield was found in the variants in which the ultrasonication lasted from 150 s to 200 s, and this yield was from 534 ± 16 mL CH4/g VS to 561 ± 17 mL CH4/g VS. The data analysis confirmed strong correlations between the pretreatment time, the amount of biogas and methane production, and the gross energy gain. The highest net energy output and net energy gain were obtained for 150 s of sonication, and, respectively, were 4.21 ± 0.17 Wh/g VS and 1.19 ± 0.18 Wh/g VS.