Nutrition is fundamental to the prevention and management of non-communicable diseases (NCDs), and health professional students are anticipated to have adequate knowledge to promote evidence-based dietary practices. However, evidence on nutrition knowledge and its determinants among health students in Zanzibar remains limited. This study assessed nutrition knowledge, practice and awareness regarding the role of nutrition in NCD prevention and identified associated factors among health students in Unguja, Zanzibar. A cross-sectional study was conducted among 503 students from four higher learning institutions. Data was collected using an online and offline self-administered questionnaire. Descriptive statistics summarized participant characteristics, knowledge levels, practical ability, and awareness of evidence-based guidelines. Chi-square tests assessed associations, and ordinal logistic regression (proportional odds model) identified predictors of nutrition knowledge, including age, gender, institution, current enrollment in a nutrition course, and prior formal nutrition training. Adjusted odds ratios (AORs) with 95% confidence intervals (CIs) were reported at a significance level of p < 0.05. Overall, 61.43% of students demonstrated moderate nutrition knowledge, while 49.30% reported a moderate ability to apply it in practice. Awareness of evidence-based nutrition guidelines was similarly moderate (61.23%). Prior participation in a nutrition course was significantly associated with practical application (p = 0.0005), and gender was associated with awareness level (p = 0.0018). Students not currently enrolled in a nutrition course had lower odds of higher nutrition knowledge (AOR = 0.57, 95% CI: 0.38–0.85; p = 0.006). Compared with students from the State University of Zanzibar, those from Zanzibar School of Health had lower odds of higher knowledge (AOR = 0.46, 95% CI: 0.30–0.70; p < 0.001). Age and gender showed no significant association with knowledge. Strengthening nutrition curricula and enhancing exposure to evidence-based guidelines and practical competencies are essential for preparing Zanzibar’s future health workforce to effectively contribute to NCD prevention and management.