This study investigates the metabolic responses of cancerous (RCC) and non-cancerous (HK2) kidney cells to treatment with Staurosporine (STAU), which has a pro-apoptotic effect, and Bongkrekic acid (BKA), which has an anti-apoptotic effect, individually and in combination, using ¹H NMR metabolomics to identify metabolite markers linked to mitochondrial apoptotic pathways. BKA had minimal metabolic effects in RCC cells, suggesting its role in preserving mitochondrial function without significantly altering metabolic pathways. In contrast, STAU induced substantial metabolic reprogramming in RCC cells, disrupting energy production, redox balance, and biosynthesis, thereby triggering apoptotic pathways. The combined treatment of BKA and STAU primarily mirrored the effects of STAU alone, with BKA showing little capacity to counteract the pro-apoptotic effects. In non-cancerous HK2 cells, the metabolic alterations were far less pronounced, highlighting key differences in the metabolic responses of cancerous and non-cancerous cells. RCC cells displayed greater metabolic flexibility, while HK2 cells maintained a more regulated metabolic state. These findings emphasize the potential for targeting cancer-specific metabolic vulnerabilities while sparing non-cancerous cells, underscoring the value of metabolomics in understanding apoptotic and anti-apoptotic mechanisms. Future studies should validate these results in vivo and explore their potential for personalized treatment strategies.