Heavy metal (HM) contamination of soils is a worldwide problem with adverse consequences to the environment and human health. For the safe production of vegetables in contaminated soil, efficient soil amendments need to be applied such as nano-hydroxyapatite (n-HAP) and poly γ-glutamic acid (γ-PGA), which can mitigate heavy metal uptake and enhance crop yield. However, the combined effects of soil amendments and indigenous microorganisms (IMOs) on HMs immobilisation and accumulation by crops have received little attention. We established a pot experiment to investigate the effects of IMOs combined with n-HAP and γ-PGA on coriander (Coriandrum sativum L.) growth and its Cd and Pb uptake in two acidic soils contaminated with HMs. The study demonstrated that applying n-HAP, with and without IMOs, significantly increased shoot dry biomass and reduced plant Cd and Pb uptake and diethylenetriaminepentaacetic acid (DTPA) extractable Cd and Pb concentrations in most cases. However, γ-PGA, with and without IMOs, only reduced soil DTPA-extractable Pb concentrations in slightly contaminated soil with 0.29 mg/kg Cd and 50.9 mg/kg Pb. Regardless of amendments, IMOs independently increased shoot dry biomass and soil DTPA-extractable Cd concentrations in moderately contaminated soil with 1.08 mg/kg Cd and 100.0 mg/kg Pb. A synergistic effect was observed with a combined IMOs and n-HAP treatment, where DTPA-extractable Cd and Pb concentrations decreased in slightly contaminated soil compared with the independent IMOs and n-HAP treatments. The combined treatment of γ-PGA and IMOs substantially increased shoot dry biomass in moderately contaminated soil. These results indicate that solo n-HAP enhanced plant growth and soil Cd and Pb immobilisation, and mitigated Cd and Pb accumulation in shoots. However, the combination of n-HAP and IMOs was optimal for stabilising and reducing HMs’ uptake and promoting plant growth in contaminated soil, suggesting its potential for safe crop production.