Fecal microbiota transplantation (FMT) modifies gut bacterial composition and improves metabolic outcomes in subjects with obesity and type 2 diabetes (ObT2), but bacterial changes alone do not fully explain the heterogeneity in clinical response. We performed virus-like particle (VLP)-enriched metagenomic sequencing coupled with bulk-DNA metagenomic sequencing on longitudinal fecal samples from a randomized controlled FMT trial in ObT2. Using random forest classification, post-FMT virome changes showed accuracy comparable to bacteriome changes (84.8% vs 81.4%) in distinguishing LDL responders from non-responders. Donor-derived viral contig engraftment was detected in 64.7% (11/17) of recipients receiving FMT alone and 58.8% (10/17) receiving FMT with lifestyle intervention (LSI), versus 5.6% (1/18) in the sham with LSI group. FMT was associated with increased virome diversity, compositional shifts toward the donor virome, and coordinated virus-bacteria associations, with most responsive viral contigs classified as Caudoviricetes . FMT-responsive viral contigs that were shared between the two FMT groups were predicted to infect Roseburia and Bifidobacterium , while contigs associated with clinical responses were predicted to infect Escherichia , Roseburia , Blautia , and Enterococcus . These findings suggest that the gut virome is a complementary ecological component associated with FMT responses and metabolic outcomes in ObT2.