Although Life Skills programs showed to improve the psychological and physical wellbeing of individuals, little attention has been paid, worldwide and in the Arab countries in specific to implementing life skills intervention for university students. In this study, we tested the effectiveness of a life skills based health promotion intervention KHOTWA (STEP) in enhancing the wellbeing of university students in Lebanon, a country that faces economic and political instability. This is a quasi-experimental study, with pre and post-test, intervention-control design. Each group was formed of 78 participants studying in a private university in Lebanon. Mixed design was used to address the process and outcomes objectives of the intervention. The program was carried online due to COVID-19 pandemic. Significant differences were observed between the intervention and the control groups for life skills, dietary habits and mental health scores at the 3-month follow-up. For the intervention group, a significant increase was observed in the mean score of each of the following Life Skills subscales: self-care ( p = 0.001), work and study ( p = 0.013), career and education planning ( p = 0.011) and looking forward/goal settings ( p < 0.001). Students also achieved a healthier eating habit compared to those in the control group by decreasing their consumption of processed food. There was no significant effect in terms of body mass index ( p = 0.827). Also, there was a significant change in the mental health status ( p = 0.012) only in the intervention group as its mean score decreased after 3 months of the intervention implementation. This intervention enhances the mental health and promotes healthy habits leading consequently to a better quality of life and more productivity amongst university students. Therefore, such interventions should be replicated in other similar context to improve university students’ well-being.