Current study was designed to extract phytochemical compounds, thymoquinone (TQ) and thymohydroquinone (THQ) from indigenous herbs i.e., Nigella sativa (seeds) and Thymus vulgaris (aerial parts). Extracted compounds were further subjected to evaluate their anti-proliferative and anti-inflammatory activities and loaded in novel biodegradable drug carrier system including pectin and poly lactide-co-glycolide (PLGA) to achieve a controlled drug release system. Drug carrier system was synthesized by extracting pectin from waste peels of citrus fruits (lemon, orange and grape fruit). To enhance the stability, FDA approved PLGA drug carrier was physically cross-linked with pectin hydrogel. This may potentially introduce an opportunity to utilize organic waste in pharmacology.Results showed that soxhlet extraction at ratio of n-hexane: methanol (1:4) has been the appropriate combination to extract maximum yield of TQ from N. sativa (56.13%) and T. vulgaris (22%). THQ extraction was not achievable due to its very less stability. HPLC quantification of essentials oil of N. sativa showed higher amount of TQ i.e., 368.55±0.12 mg/kg (Mean±SEM) and T. vulgaris had 197.58±0.7 mg/kg. The pectin was successfully extracted in maximum yield from waste peels of lemon as compared to other two samples i.e., 35.3±0.66 g (Mean±SEM). Characterization of pectin extracted from each samples showed orange pectin potentially more suitable for hydrogel formation. SEM analysis confirmed the nanoparticles of TQ efficaciously produced loaded in PLGA-PEG at average size of 280 nm. TQ has been proved to be potent anti-proliferative and anti-inflammatory agent by in-vivo antioxidant assays (DPPH and FRAP assay), MTT assay against HeLa cancer cell line and SRB assay against HCT116 colon cancer cell line. Inhibition concentration (IC50) of TQ against HeLa and HCT116 cancer cell lines showed less significant difference (p > 0.05) to the IC50 of control commercial anti-cancer drug (cisplatin). TQ and its nanoparticles loaded in pectin hydrogel showed delayed release of TQ thus enabling the controlled drug release from 24 to 72 hours. TQ thus obtained can be utilized against early treatments of variety of cancers as can be observed from IC50 obtained against HeLa and HCT116 cancer cell lines. Findings of the current study indicate the potential of local resources in effectiveness against cancer. Therefore, increased incidences of cancer can be reduced among impoverished areas.