The isolation of Candida may be related to comorbidity, prolonged mechanical ventilation, and survival during intensive care unit (ICU) stay, especially with non-albicans Candida (NAC). To examine the frequency of Candida isolation, associated comorbidities and outcomes in the surgical ICU in Osijek University Hospital, Croatia, the data from the electronic database from May 2016 to 30 June 2023 were analyzed. In a cross-sectional study examining 15,790 microbiological samples, different strains of Candida were observed in 581 samples from 236 patients. The control group (N = 261) was 130 consecutive patients from March to May 2019 and 131 in the same months in 2020 (pre- and post-COVID-19). Comorbidities, duration of mechanical ventilation, and survival were compared. Patients with isolated Candida were more often non-elective and had significantly more heart, kidney, and liver diseases and sepsis than the control group (p < 0.001). The duration of mechanical ventilation was 9.2 [2.2–9.24], 96 [24–146], 160 [19.5–343], and 224 [73.5–510] hours in the controls, in patients with Candida albicans, in patients with NAC, and in patients with ≥2 Candida species isolated, respectively. The mortality was significantly higher (42%) in patients with isolated Candida than in the control group (19%, p < 0.001). In a multivariate analysis adjusted for patients’ age, the Simplified Acute Physiology Score II, days of ICU, and type of admission, only sepsis on admission was an independent predictor of mortality (odds ratio = 2.27).