Nanotechnology is a rapidly evolving scientific field due to advantages such as improved bioavailability, enhanced bioactivity and targeted drug delivery. However, concerns exist regarding its potential toxicity, as nanoparticles can enter the biological systems and induce inflammatory responses, oxidative stress, neurotoxicity and genotoxicity. These risks necessitate comprehensive toxicological evaluations to ensure their safe biomedical use. Green synthesis, particularly using citrus fruit peels, presents an eco-friendly alternative for nanoparticle production by leveraging bioactive compounds to reduce toxicity. This study aimed to assess the embryonic toxicity of citrus fruit (Citrus reticulata and C. limonum) peel-mediated hydroxyapatite nanocomposites, providing insights into their safety and guiding future research toward sustainable nanotechnology applications. Green synthesis of C. reticulata and C. limonum-mediated hydroxy apatite nanocomposites was successfully carried out. The toxicity of developed nanocomposite was assessed using embryonic toxicology evaluation in zebrafish. Stereo microscopic analysis was done for the assessment of morphologic features, developmental stages and potential malformation of zebrafish embryos. At a 24 hr interval, hatching rate and embryonic viability rates were measured. Sublethal toxicity was observed in the zebrafish embryonic toxicology evaluation, with a dose-dependent hatching rate and embryonic viability. Overall, C. reticulata and C. limonum-mediated hydroxyapatite nanocomposites exhibited very low toxicity based on zebrafish embryonic toxicology evaluations.