A sequencing batch reactor (SBR) inoculated with activated sludge and bioaugmented with a dye-decolorizing yeast strain—Yarrowia lipolytica (HOMOGST27AB) was assembled to form yeast-bioaugmented aerobic granular sludge (AGS). The bioaugmented AGS-SBR was operated for the treatment of synthetic saline wastewater (12 g L−1) intermittently fed with a reactive textile dye (Navy Everzol ED) at 25, 15, and 7.5 mg L−1. Dye degradation did not occur, although some dye adsorbed to the granules. AGS-SBR performance in removing carbon and nitrogen was good and was not affected by the dye addition. Bioaugmentation with the yeast Y. lipolytica (HOMOGST27AB) occurred with success, proved by sequencing samples from granules throughout the reactor operation. The AGS core microbiome gathered essentially microorganisms from the Proteobacteria and Bacteroidetes phyla. The microbial profile showed a dynamic microbiome established at Phase I of the operation, with a high decrease in the abundance of Ignavibacterium from the initial biomass to the granules formed and an increase in Actinobacteria, Cytophagia, Flavobacteria, and Alphaproteobacteria in the remaining phases of the bioreactor operation.