Parkinson's disease (PD) and Alzheimer's disease (AD) consist of progressive illnesses of central nervous system that primarily affect the elderly and are characterized by movement symptoms, memory decline, and cognitive impairment. A number of variables, including the lack of a novel treatment, a steady rise in the patient population, and the high expense of care and treatment, have contributed to the growing significance of these diseases. In recent decades, we have gained a better understanding of the causes of diseases, but complex mechanisms of neuronal loss, combined with physiological factors that are incompatible, pose challenges in describing the pathogenic processes and devising effective treatments. Currently, there are no known treatments for most of these diseases, rendering them incurable. Therefore, there is a pressing need for therapeutic interventions that have the potential to effectively treat neurodegeneration. This study aimed to evaluate the efficacy of the ayurvedic herb Bacopa monnieri bioactive components against the therapeutic targets HTR1A, HTR1B, HTR2A, HTR2C, HTR7, alpha-synuclein, amyloid beta, and tau protein of Alzheimer's and Parkinson's illnesses. The docking analysis revealed the promising binding affinity with Quercetin, Apigenin, and Luteolin and Molecular mechanics/generalized Born surface area (MM/GBSA) further confirmed the stability of the complexes. In vitro investigation indicated that Quercetin is the most effective for treating AD and PD due to its considerable inhibition of alpha-synuclein production, whereas Luteolin is the favorable one for preventing both diseases by mitigating effects during Rotenone treatment. The future implications and constraints of the current study suggest that further validation in Invivo models of Alzheimer's and Parkinson's diseases is necessary to investigate the effects of Quercetin and Apigenin in the treatment of these conditions, as well as Luteolin and Quercetin for their prevention.Supplementary InformationThe online version contains supplementary material available at 10.1007/s13205-025-04224-6.