Membrane bioreactors (MBRs) are used for the treatment of piggery wastewater. In this study, we investigated the microbiomes of sludge and membrane-attached biofilm in MBRs treating piggery wastewater by non-destructive confocal reflection microscopy and high-throughput sequencing of 16S rRNA genes. Microscopic visualization indicated that amine-containing extracellular matrix accumulating on the membrane caused membrane fouling, especially in the absence of microbiome acclimatization. The principal coordinate and phylogenetic analyses of the sequence data showed that the sludge and biofilm microbiomes were different, but that both changed in response to reactor conditions. The non-acclimatized sludge microbiomes were composed of operational taxonomic units (OTUs) that were abundant in piggery wastewater. The acclimatized microbiomes, including the polysaccharide-degrading Mitsuaria chitosanitabida and protein-degrading Reyranella massiliensis, were found under stable conditions. An OTU related to the bacteriolytic myxobacterium Enhygoromyxa salina increased under the deteriorative condition induced by overloading. Meanwhile, the biofilm microbiomes comprised mainly phylogenetically novel bacteria under all conditions. In addition, the anaerobic Clostridium cellulovorans became dominant in the thick, dense biofilms observed under the deteriorative condition. The results of this study demonstrated that sludge and biofilm microbiomes are associated with reactor performance, especially with membrane fouling, during MBR treatment of piggery wastewater.