Exploration of possible pharmacological effects along with characterisation of the bioactive compounds present in peels may have a key role in converting the fruit waste materials into therapeutic value added products. Extracts prepared from the Citrus limetta fruit peels were studied for antioxidant and anti- inflammatory activity using in-vitro bioassays. Among all, ClEt an ethanol extract of Citrus limetta fruit peels has shown promising anti-oxidant and anti-inflammatory activity. ClEt was further validated to ensure its safety evaluation at 2000mg/kg and anti-malarial efficacy at 100, 250, 500 mg/kg body weight with special reference to inflammatory mediators involved in malaria pathogenesis. In-vivo study revealed that ClEt was safe at higher dose and showed promising anti-malarial activity by inhibiting the parasitaemia and inflammatory mediators (IFN-γ, TNF-α, IL-6) involved in malaria pathogenesis, able to improve the haemoglobin and glucose level and increase the survival time. Chemical fingerprint of ClEt revealed the presence of flavonoids. Results suggested the suitability of ClEt, a flavonoid rich fraction of Citrus limetta fruit peels as a candidate for further investigation towards the management of malaria pathogenesis.