The growing consumption of poultry meat has spurred the development of meat-processing plants and an associated rise in wastewater generation. Anaerobic digestion is one of the preferred processes for treating such waste. The current push towards biogas upgrading and out-of-plant use necessitates new, competitive ways of heating digesters. One such alternative is to use electromagnetic microwave radiation (EMR). The aim of the study was to assessment how EMR used as a heat source impacts the anaerobic processing of high-load poultry slaughterhouse wastewater (H-LPSW) and its performance. Microwave heating (MWH) was found to boost the CH4 fraction in the biogas under mesophilic conditions (35 °C) as long as the organic load rate (OLR) was maintained within 1.0 kgCOD/dm3·d to 4.0 kgCOD/dm3·d. The best performing variant—EPM heating (55 °C), OLR = 3.0 kgCOD/dm3·d, HRT = 5 days—produced 70.4 ± 2.7% CH4. High COD and TOC removal, as well as the highest biogas yields, were achieved for loadings of 1.0 gCOD/dm3·d to 4.0 gCOD/dm3·d. Effluent from the EMR-heated reactors (1.0 gCOD/dm3·d) contained, on average, 0.30 ± 0.07 gO2/dm3 at 55 °C and 0.38 ± 0.10 gO2/dm3 at 35 °C. The corresponding COD removal rates were 97.8 ± 0.6% and 98.1 ± 0.4%, respectively. The 5.0 gCOD/dm3·d and 6.0 gCOD/dm3·d OLR variants showed incremental decreases in performance. Based on the polymerase chain reaction results of 16S rDNA analysis, diversity of bacterial communities were mostly determined by OLR, not way of heating.