Candida kefyr (Kluyveromyces marxianus), an ascomycetous environmental yeast, occasionally isolated from dairy products, represents an uncommon but emerging pathogen in immunocompromised patients. Herein, we present a case of C. kefyr pyelonephritis in a 41-year-old, previously immunocompetent, patient who was hospitalized in an COVID-19 ICU. Pyelonephritis was associated with caliectasis and obstruction due to possible fungus ball formation. Predisposing factors included ICU stay, use of broad spectrum antibiotics and steroids, central venous catheterization, mechanical ventilation and urologic manipulation. Susceptibility testing revealed high MIC values to amphotericin B. Infection was effectively controlled by prolonged administration of fluconazole without further surgical intervention. COVID-19 complicated with invasive candidiasis is an increasingly observed clinical situation that warrants high suspicion index and careful evaluation of laboratory data.