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Colorectal cancer (CRC) is a growing public health challenge, featuring a multifactorial etiology and complex host–environment interactions. Recently, increasing evidence has pointed to the role of the gut microbiota in CRC development and progression. To explore the role of gut microbes in CRC, we retrieved metagenomic data from 156 stools from the European Nucleotide Archive database and mapped them against the VFDB database for virulence factors (VFs). GO annotations of VFs and KEGG pathways were then performed to predict the microbial functions and define functional pathways enriched in the tumor-associated microbiota. Interestingly, 306 VFs were detected in the metagenomic data. We revealed the enrichment of adenomas with VFs involved in cell adhesion, whereas in the early stages of CRC they were enriched in both adhesins and isochorismatase. Advanced stages of CRC were enriched with microbial siderophores, especially enterobactin, which was significantly associated with isochorismate synthase. We highlighted higher abundances of porins and transporters involved in antibiotic resistance and the development of biofilm in advanced stages of CRC. Most VFs detected in CRC, particularly in advanced stages, were shown to be included in siderophore biosynthesis pathways. This enrichment of predicted VFs supports the key role of the gut microbiota in the disease.