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Several studies have demonstrated that malnutrition is a negative prognostic factor for clinical outcomes. However, there is limited evidence for the effect of malnutrition on clinical outcomes in patients with candidemia. We investigated the relationship between malnutrition and all-cause 28-day mortality among patients with non-<i>albicans</i> candidemia. Between July 2011 and June 2014, all adult patients with non-<i>albicans</i> candidemia, including <i>C. tropicalis</i>, <i>C. glabrata</i>, <i>C. parapsilosis</i> and so on, were enrolled. The Malnutrition Universal Screening Tool (MUST) scores were used to determine the patients’ nutritional status before the onset of candidemia. A total of 378 patients were enrolled; 43.4% developed septic shock and 57.1% had a high risk of malnutrition (MUST ≥ 2). The all-cause 28-day mortality rate was 40.7%. The Cox proportional hazards model revealed that <i>C. tropicalis</i> (HR, 2.01; 95% CI, 1.24–3.26; <i>p</i> = 0.005), Charlson comorbidity index (HR, 1.10; 95% CI, 1.03–1.18; <i>p</i> = 0.007), Foley catheter use (HR, 1.68; 95% CI, 1.21–1.35; <i>p</i> = 0.002), concomitant bacterial infections (HR, 1.55; 95% CI, 1.11–2.17; <i>p</i> = 0.010), low platelet count (HR, 3.81; 95% CI, 2.45–5.91; <i>p</i> < 0.001), not receiving antifungals initially (HR, 4.73; 95% CI, 3.07–7.29; <i>p</i> < 0.001), and MUST ≥ 2 (HR, 1.54; 95% CI, 1.09–2.17; <i>p</i> = 0.014) were independently associated with all-cause 28-day mortality. A simple screening tool for nutritional assessment should be used for patients with non-<i>albicans</i> candidemia to detect early clinical deterioration, and a tailored nutritional care plan should be established for malnourished individuals, to improve their clinical outcomes.