Background: Candida species are opportunistic fungal pathogens that frequently colonize the gastrointestinal tract of immunocompromised individuals, including people living with HIV (PLHIV). Gastrointestinal Candida colonization has been associated with persistent diarrhea and poor health outcomes. Despite the high burden of HIV/AIDS in Ecuador, there is limited research on Candida prevalence and antifungal resistance patterns in this population. This study aimed to determine the prevalence of Candida species in HIV-positive individuals with diarrhea and assess associations with clinical and immunological parameters. Methods: A descriptive, cross-sectional study was conducted at the José Daniel Rodríguez Infectious Hospital in Guayaquil, Ecuador, between April 2021 and May 2022. The study included 85 HIV-positive adults with diarrhea, categorized into those with and without Candida colonization. Fecal samples were analyzed using culture, microscopy (Gram staining, SEM, immunofluorescence), Sabouraud Glucose Agar and CHROMagar™ Candida for species identification. Antifungal susceptibility testing was performed using the VITEK^® 2 Compact system following EUCAST guidelines. Due to the small sample size, only descriptive statistical analyses were performed. Results: The Candida species were detected in 64 of 85 patients (75.3%), with Candida albicans being the most prevalent species. Candida colonization was associated with severely low CD4 counts (<200 cells/µL, 71.0%), high viral loads (≥10,000 copies/mL, 46.6%), and poor ART adherence (55.3%). Antifungal susceptibility testing showed 94.5% fluconazole resistance (SEN1), while all isolates remained 100% sensitive to caspofungin (SEN4, SEN5, SEN6). Conclusions: This study highlights a high prevalence of Candida colonization in HIV-positive individuals with diarrhea, particularly those with advanced immunosuppression and poor ART adherence. The high levels of fluconazole resistance raise concerns about the efficacy of current antifungal treatments, suggesting a need for routine antifungal susceptibility testing. Given the study’s descriptive nature and single-site design, further research with larger, multicentric cohorts is needed to improve clinical management and antifungal stewardship.