Apples contain bioactive compounds with the potential to alleviate clinical signs associated with obesity, a phenomenon likely related to the composition and function of the gut microbiota. The aim of this study was to investigate the effect of apple supplementation on the fecal microbiota and gut metabolites of Dawley Sprague rats fed a high-fat (HF group) or a low-fat (LF group) diet. The fecal microbiota was examined using 16S marker sequencing targeting the V4 region in a MiSeq instrument (Illumina). With the exception of Blautia, which was higher in supplemented rats compared to controls within the LF group, significant differences in fecal microbiota between supplemented rats and controls were only found in the HF group. This suggests that the effect of apple supplementation on the gut microbiota is strongly dependent on the composition of the diet, a phenomenon with potential consequences for obese human patients. Principal Coordinate Analysis of unweighted UniFrac distances revealed a clear strong separation of bacterial communities based on diet (HF and LF, P = 0.001, R = 0.69, ANOSIM test) and based on apple supplementation within the HF group, albeit less strongly (P = 0.006, R = 0.27, ANOSIM test). No differences were found for fecal SCFAs but proteomics and metabolomics analyses showed differential expression of both proteins and metabolites between supplemented rats and controls in the HF group. The results of this study can guide future explorations of the effect of apple supplementation on human health.