Oleaginous yeast lipid derived fatty acid methyl esters (FAMEs) are renowned for their exceptional potential towards bioenergy production specially in biodiesel domain. FAME application in other realms of biotechnology including nanotechnology (offer large possibilities for industry and contemporary science) has hitherto remained unexplored. Present study has investigated the novel use of FAME as biogenic capping agents to synthesize amphotericin B loaded CuO-CT (CT: chitosan) nanocomposites. The utilization of FAME-modified formulation (CuO-CTY@.L.F-AmpB) is evident in providing steric stability, as indicated by various physiochemical characterization techniques, accompanied by a low polydispersity index 0.24 ± 0.06 and a partial negative surface charge. Additional insights from HRTEM reveal a nanocarrier with a rod-shaped morphology, featuring 40–50 nm length and a 5–6 nm diameter. Amphotericin B release from CuO-CT@Y.L.F-AmpB followed a sustained pattern for up to 100 h, suggested FAME coating facilitated the drug release for a longer time duration. FAME stabilization has improved antibiofilm activity against Candida albicans (BEC50: 15 μg/mL) evinced by multitude assays that were found concordant with each other. A comprehensive FAME profiling conducted through GC-MS unveiled the predominance of oleic (84.02 ± 0.30 %) and palmitic acid methyl esters (9.40 ± 0.15 %) in the sample. This observation identifies them as concealed factors contributing to the stability of the nanocomposite. Conclusively, present study stipulated FAME as an efficient capping agent where it impart stability as well as efficacy to the nanocarrier. Moreover, current research work opens an innovative path for biorefinery approach integrating simultaneous production of lipid and multiphase nano-material synthesis, vital for a sustainable and circular bio-economy.