The aim of this study was the performance evaluation of anaerobic digestion of dairy wastewater in a multi-section horizontal flow reactor (HFAR) equipped with microwave and ultrasonic generators to stimulate biochemical processes. The effects of increasing organic loading rate (OLR) ranging from 1.0 g chemical oxygen demand (COD)/L·d to 4.0 g COD/L·d on treatment performance, biogas production, and percentage of methane yield were determined. The highest organic compounds removals (about 85% as COD and total organic carbon—TOC) were obtained at OLR of 1.0–2.0 g COD/L·d. The highest biogas yield of 0.33 ± 0.03 L/g COD removed and methane content in biogas of 68.1 ± 5.8% were recorded at OLR of 1.0 g COD/L·d, while at OLR of 2.0 g COD/L·d it was 0.31 ± 0.02 L/COD removed and 66.3 ± 5.7%, respectively. Increasing of the OLR led to a reduction in biogas productivity as well as a decrease in methane content in biogas. The best technological effects were recorded in series with an operating mode of ultrasonic generators of 2 min work/28 min break. More intensive sonication reduced the efficiency of anaerobic digestion of dairy wastewater as well as biogas production. A low nutrient removal efficiency was observed in all tested series of the experiment, which ranged from 2.04 ± 0.38 to 4.59 ± 0.68% for phosphorus and from 9.67 ± 3.36 to 20.36 ± 0.32% for nitrogen. The effects obtained in the study (referring to the efficiency of wastewater treatment, biogas production, as well as to the results of economic analysis) proved that the HFAR can be competitive to existing industrial technologies for food wastewater treatment.