A multicentre, laboratory-based analysis was conducted on aggregated data from 23 hospitals across Colombia. Of 1761 fungal isolates identified, 1642 were yeasts and constitute the focus of this study. Isolates were identified using the VITEK^®2 system, with confirmatory identification by MALDI-TOF-MS for a subset. Antifungal susceptibility testing for fluconazole, voriconazole, amphotericin B, and the echinocandins was performed on Candida albicans, C. parapsilosis, and C. tropicalis. Data were stratified by clinical service: adult ICU, adult wards, paediatric ICU, neonatal ICU, and paediatric wards. Temporal trends were assessed using the Cochran–Armitage test. The most prevalent species were C. albicans (42%), C. parapsilosis (24%), C. tropicalis (11%), C. glabrata (7%), and C. auris (3%). C. albicans predominated in adult services, whereas C. parapsilosis was the leading pathogen across paediatric settings. Among species with validated breakpoints, the overall fluconazole resistance rate was 19%, driven primarily by C. parapsilosis (35%, exceeding 40% in some clinical services). Non-wild-type to voriconazole and amphotericin B was low (<5%), and echinocandin resistance was exceedingly rare. The substantial fluconazole resistance driven by C. parapsilosis, together with the emergence of C. auris, underscores the urgent need for sustained surveillance and species-directed antifungal stewardship programmes.