Abstract Introduction Khalwa is an Islamic educational institution, known as such in Sudan and called elsewhere Koranic institution. Our research aimed to assess the nutritional status and its related factors among Khalwa residents in Khartoum State. Methods A facility-based cross-sectional study was implemented in two localities of Khartoum State. A multistage sampling technique was used to selected 1273 residents. At first level, four khalwa were selected in the seven localities of Khartoum State through a stratified random sampling technique. At second level, in each of the khalwa selected, all the residents fulfilling the inclusion and exclusion criteria were included in the study. The collected data were firstly summarized numerically and graphically. Then, associations/differences among variables were determined through chi-square tests and ANOVA. A multinomial logistic regression established the relationship between the nutritional status of the residents and its related factors. All statistical tests were considered statistically significant when p < 0.05. Results The age of 1273 residents varied from 6 to 60 years with an average age of 15 years. Their mean body mass index (BMI) of 16.6±3.4 ranged from 7.8 to 34.0. 73.8% (939/1272) of the residents were undernourished, 23.9% (23.9%, 309/1272) were well nourished and 2.3% (29/1272) were overweight/obese. The statistically significant factors related to the nutritional status of the residents were age (under-nourished p =0.000; well-nourished p= 0.004), status in the khalwa ( p =0.001 vs p =0.075), resting time ( p =0.002 vs p =0.038), practices of hand washing ( p =0.165 vs p =0.011) and exercising ( p =0.032 vs p =0.027). The food practices, despite their contributions to the model, were not statistically significant (p > 0.05). Discussion The nutritional status of khalwa should be translated urgently in a community-directed intervention based on a partnership involving the affected communities, political and administrative authorities, national, bilateral and international donors to overcome the burden of malnutrition.