Purpose Smartphone is an impending solution to influence long-term behavior change, including physical activity; however, the evidence regarding personalized prescription remains mixed in obese. We aimed to explore the influence of smartphone-based physical activity promotion on weight loss and cognitive functions in obese young adults. Methods In our pilot randomised controlled trial, 24 obese adults were randomized to two conditions: (1) EXI group receiving a smartphone-application based personalized physical activity prescription; (2) CONT group continuing their routine work for eight weeks. Executive functions and cardiometabolic risk variables [body and fat mass, waist circumference (WC), blood pressure (BP)] and executive functions were measured before and after eight weeks. Results Our study findings revealed a significant improvement in reaction times with overall (H = 7.71, p = 0.005), congruent stimuli (H = 4.43, p = 0.03) and incongruent stimuli (H = 5.35, p = 0.02) between groups. Though EXI participants reduced their fat mass by 5.07 kg more than CONT group users after eight weeks, the findings were statistically insignificant. Similarly, our study did not find significant differences in body mass, WC, BP or accuracy between EXI and CONT groups. There was a decreased user engagement (H = 5.80, p = 0.564) after the 3rd week of the study period. Conclusion Short-term smartphone-based physical activity programs may offer favourable cognitive benefits to young adults; however, the weight loss benefits remain unconvincing. Trial Registration The study was registered prospectively with the Clinical Trials Registry of India (CTRI/2022/02/040202).