Fecal microbiota transplantation (FMT) from a healthy donor to recurrent C. difficile infection (CDI) patients has proven efficient in curing the disease, possibly through bacteriophage-mediated (phages) modulation of the gut microbiome landscape. Fecal virome transplantation (FVT, sterile filtrated donor feces) has also been shown efficient for treating the disease. FVT has the advantage over FMT that no bacteria are transferred, but FVT does not exclude the risk of transferring eukaryotic viruses. We aimed to develop methodologies to obtain safer FVT by removing and/or inactivating eukaryotic viruses, while maintaining an active phage community. Donor feces were used as inoculum for a chemostat-fermentation to remove eukaryotic viruses by dilution (FVT-ChP). FVT solutions underwent solvent-detergent treatment to inactivate enveloped viruses (FVT-SDT) and pyronin-Y treatment to block the replication of RNA-viruses (FVT-PyT). The efficacy of these treatments was assessed in a CDI mouse model and compared with untreated FVT (FVT-UnT), FMT, and saline-treatment as controls. Intriguingly, 8/8 mice receiving FVT-SDT did not reach the humane endpoints until planned euthanization and expressed limited symptoms of CDI. While 5/7 saline treated mice reached the humane endpoint. Compared to the saline treatment, lower C. difficile abundance (p<0.005) in the FVT-SDT-treated mice suggested that the intervention had hampered C. difficile colonization. The mice receiving FVT-ChP and FVT-UnT tended to express alleviated CDI symptoms compared to the saline control. This proof-of-concept study may constitute the initial step of developing therapeutic tools that targets a broad spectrum of gut-related diseases and thereby substituting FMT with a safer phage-mediated therapies.