The goal of this study was to use natural phosphate (NP) abundant in Algeria, as an adsorbent for the removal of uranium (VI) from aqueous solutions in batch adsorption. A full 23 factorial extended experimental design was investigated. The factors and levels used during the experiments were; pH (X1) (1–5), initial U(VI) concentration (X2) (30–60 mg L−1) and adsorbent dose (X3) (5–30 g L−1). The properties of NP were characterized by XRF, SEM, EDS, XRD and FTIR before and after adsorption. The effects of factors were explored by response surface methodology. The equilibrium data of U(VI) adsorption onto NP fitted to the Langmuir − 1 model at a maximum monolayer capacity of 11.11 mg g−1 with the kinetics being pseudo-second-order. The characterization of the filtered solid after adsorption revealed the formation of a new lamellar crystal phase of autunite Ca(UO2)2(PO4)2(H2O)6. The calculated value of the mean free energy indicates the chemisorption process. Under optimal conditions, the uranium effluent derived from the precipitation of ammonium uranyl carbonate removal performance of 100% was achieved.