Indicators to predict healthcare-associated infections (HCAI) are scarce. Malnutrition is known to be associated with adverse outcomes in healthcare but its identification is time-consuming and rarely done in daily practice. This cross-sectional study assessed the association between dietary intake, nutritional risk, and the prevalence of HCAI, in a general hospital population. Dietary intake was assessed by dedicated dieticians on one day for all hospitalized patients receiving three meals per day. Nutritional risk was assessed using Nutritional Risk Screening (NRS)-2002, and defined as a NRS score ≥ 3. Energy needs were calculated using 110% of Harris-Benedict formula. HCAIs were diagnosed based on the Center for Disease Control criteria and their association with nutritional risk and measured energy intake was done using a multivariate logistic regression analysis. From 1689 hospitalised patients, 1024 and 1091 were eligible for the measurement of energy intake and nutritional risk, respectively. The prevalence of HCAI was 6.8%, and 30.1% of patients were at nutritional risk. Patients with HCAI were more likely identified with decreased energy intake (i.e. ≤ 70% of predicted energy needs) (30.3% vs. 14.5%, P = 0.002). The proportion of patients at nutritional risk was not significantly different between patients with and without HCAI (35.6% vs.29.7%, P = 0.28), respectively. Measured energy intake ≤ 70% of predicted energy needs (odds ratio: 2.26; 95% CI: 1.24 to 4.11, P = 0.008) and moderate severity of the disease (odds ratio: 3.38; 95% CI: 1.49 to 7.68, P = 0.004) were associated with HCAI in the multivariate analysis. Measured energy intake ≤ 70% of predicted energy needs is associated with HCAI in hospitalised patients. This suggests that insufficient dietary intake could be a risk factor of HCAI, without excluding reverse causality. Randomized trials are needed to assess whether improving energy intake in patients identified with decreased dietary intake could be a novel strategy for HCAI prevention.