Dealing with the current defaults of environmental toxicity, heating, waste management, and economic crises, exploration of novel non-edible, toxic, and waste feedstock for renewable biodiesel synthesis is the need of the hour. The present study is concerned with Buxus papillosa with seeds oil concentration (45% w/w), a promising biodiesel feedstock encountering environmental defaults and waste management; in addition, this research performed simulation based-response surface methodology (RSM) for Buxus papillosa bio-diesel. Synthesis and application of novel Phyto-nanocatalyst bimetallic oxide with Buxus papillosa fruit capsule aqueous extract was advantageous during transesterification. Characterization of sodium/potassium oxide Phyto-nanocatalyst confirmed 23.5 nm nano-size and enhanced catalytic activity. Other characterizing tools are FTIR, DRS, XRD, Zeta potential, SEM, and EDX. Methyl ester formation was authenticated by FTIR, GC-MS, and NMR. A maximum 97% yield was obtained at optimized conditions i.e., methanol ratio to oil (8:1), catalyst amount (0.37 wt%), reaction duration (180 min), and temperature of 80 °C. The reusability of novel sodium/potassium oxide was checked for six reactions. Buxus papillosa fuel properties were within the international restrictions of fuel. The sulphur content of 0.00090% signified the environmental remedial nature of Buxus papillosa methyl esters and it is a highly recommendable species for biodiesel production at large scale due to a t huge number of seeds production and vast distribution.