Aspergillus-derived protease and lipase, which are involved in the production of Aspergillus-fermented foods, are consumed as digestive enzyme supplements. A marked bifidogenic effect of supplemental Aspergillus protease preparation (AP) in rats fed with a high-fat diet was identified. This study was conducted to examine whether the consumption of Aspergillus-derived lipase exerts similar bifidogenic effect. Rats were fed diets supplemented with either an Aspergillus-derived lipase preparation (AL) or AP at 0.1% for two weeks. 16S rRNA gene sequencing analysis indicated that supplemental AL and AP markedly influenced cecal microbial community. At the phylum level, treatment with AL and AP resulted in a lower relative abundance of Firmicutes and Bacteroidetes, but a higher relative abundance of Actinobacteria and Proteobacteria than the control rats (p < 0.05). At the genus level, AL and AP remarkedly elevated the relative abundances of Bifidobacterium, Collinsella, and Enterococcus, but significantly reduced those of Oscillospira, Dorea, and Coprobacillus (p < 0.05). These modulations were similar to those reported by several studies with typical prebiotic oligosaccharides. Notably, the bifidogenic effect of AL was much greater than that of AP. Our results show that the two different Aspergillus-derived preparations, AL and AP, have strong bifidogenic effects and can change the microbiota’s composition.