Introduction Candida auris poses a significant healthcare challenge due to its high mortality rates, difficulties in identification, and resistance to antifungal treatment. This study aims to identify risk factors associated with 30-day mortality in patients with either invasive Candida auris infection or colonization. Methods We conducted a prospective study at Salmaniya Medical Complex, a tertiary care hospital in Bahrain, from September 2023 to February 2024. The study included 59 patients infected or colonized by Candida auris. Data were systematically collected from patient records, including demographics, clinical characteristics, and outcomes. Risk factors for 30-day mortality were analyzed using both univariate and multivariate statistical methods. Results Among the 59 patients studied, the mean age was 63.9 years, and the cohort was predominantly male (74.6%). Key findings include a high prevalence of multiple indwelling catheters (44.2%) and recent intubation (42.4%). Candida auris was most frequently isolated from the groin (33.9%) and urine (25.4%), with a notable presence in the axillary regions (23.7%). The mortality rate was 44.1%. Univariate and multivariate analyses revealed that age (≥65 years), multiple indwelling catheters, ICU admission for over 24 hours, and recent intubation were significant risk factors for mortality while chronic kidney disease did not retain its significance in the multivariate model. Conclusion The study underscores the critical need for focused infection control and strong antimicrobial stewardship to address the high mortality associated with Candida auris infections. Emphasizing the importance of early detection and a multidisciplinary approach, these strategies are essential for managing and mitigating the impact of Candida auris in healthcare settings.