AbstractThis study provides a new emphasis for research on the valorization of biowastes into nanocatalyst and biorefineries to be integrated with petroleum bioupgrading and polluted water treatment. The response surface optimized batch transesterification of waste‐frying oil using methanol and sustainable animal bone valorized fluorapatite nanocatalyst (FAP) yielded approximately 97% biodiesel via a pseudo‐second‐order reaction with an efficient rate of 0.48 (mol L−1)−1min−1 and activation energy of 13.11 kJ mol−1. In a pioneering step, by‐products of the starch industry and the biodiesel transesterification process; corn‐steep liquor (CSL 0.2 g L−1) and bioglycerol (6.24 g L−1) as nitrogen and carbon sources, increased the dibenzothiophene biodesulfurization (BDS) efficiency of a novel biodesulfurizing Rhodococcus jialingiae strain HN3 (NCBI Gene Bank Accession No. MN173539) sixfold. Further, upon the application of such bioproducts in a batch BDS process (1/3 petro‐diesel/water) of 96 h; HN3 desulfurized 82.26% of 0.62 wt.% sulfur without affecting the petro‐diesel calorific value. In an attempt to reach zero waste, an auxiliary pioneering step was performed, where the spent waste FAP, after being efficiently used for four successive transesterification cycles, was applied to photo‐remediate 4‐nitrophenol polluted water under UV‐irradiation. Advantageously, the fresh and spent waste FAP recorded the same photodegradation capabilities. Where they obeyed the Langmuir–Hinshelwood kinetic model (R2 ≥ 0.966) recording the same rate constants (kapp 0.032 min−1) and were efficiently reused for four successive polluted‐water treatment cycles. © 2021 Society of Chemical Industry and John Wiley & Sons, Ltd