Background: Malnutrition and hypertension are widespread among university students, with dietary habits and sedentary lifestyles playing significant roles. This study aimed at determining the prevalence and factors linked to malnutrition and hypertension in Southwest Nigeria’s university population. Methods: Conducted from January 2018 to December 2022, a cross-sectional study was undertaken at Lead City University in South-West Nigeria. Medical records of 5110 enrolled students were analyzed to assess the prevalence and factors associated with malnutrition and hypertension within the university population. Data encompassing demographic information and health metrics were examined for this study. Results: A study of 5110 participants, mean age (23.57+14.89), female sex (54.1%), blood group O prevalence (53.6%), Rhesus negative (4.9%), and genotype AA prevalence (73.6%). The average weight was 67.17+ 15.18 kg and height of 1.67+ 0.93 meters. Hypertension prevalence was at 8.7%, while malnutrition is 42.7%. Among the participants, 3% were anemic while the mean systolic and diastolic blood pressure were 115.93+15.26 and 73.52+17.43 respectively. Male sex was significant factor in hypertension and malnutrition (p < 0.001). PCV levels lack significant associations, while BMI categories strongly correlate with hypertension (p < 0.001). Discussion: The demographic profile reveals a youthful population vulnerable to behaviors impacting long-term health. With malnutrition prevalence at 47.2%, significant health concerns arise, while the relatively low hypertension rate of 8.7% is promising but requires ongoing monitoring. Age is a notable risk factor for hypertension, stressing targeted interventions for older adults. Sex disparities highlight the need for sex-specific healthcare. Blood group, Rhesus factor, and genotype lack significant associations with hypertension, while hypertension prevalence varies across packed cell volume levels. BMI strongly links to hypertension, highlighting obesity management’s importance. Conclusion: Understanding demographic factors and health metrics is crucial for developing effective interventions to address malnutrition and hypertension risks within populations.