The quest for natural ingredients with potent health-promoting properties has shifted focus towards bioactive compounds, enriching the healthcare and wellness industry. As artificial intelligence–based healthcare systems gradually traverse the human–technology barrier, a shift towards systems approach concerning natural compound–based drug design looms large. We summarize a range of promising bioactive ingredients from various sources, including few plants used in folk medicine and non-timber forest products (NTFPs) which are consumed in the daily diet of ethnic tribes. These diverse molecules exhibit a spectrum of beneficial properties, including antioxidant, anti-inflammatory, antimicrobial, and immune-modulating effects. Systems biology offers a spatial understanding of genomics, transcriptomics, and metabolomics to unravel the intricate networks of genes, proteins, and metabolites underlying bioactive compound production and function. Network pharmacology and systems biology in unison can aid the development of customized bioactive formulations and even the creation of synthetic biology strategies for targeted production of desired compounds. By analysing metabolic profiles, we can pinpoint molecules with specific health benefits, guiding targeted bioprospecting efforts. By unlocking nature’s secrets, such efforts would pave the way for a future where personalized, holistic approaches reign supreme, fostering a healthier and more fulfilling life for all.