Two forms of zinc-aluminium layered double hydroxides (ZnAl-LDH) with borate association (iZA and cZA) were prepared by ion-exchange process and in-situ co-precipitation. The received materials were examined using several characterization techniques, e.g. x-ray diffraction (XRD), scanning- and transmission-electron microscopy (SEM and TEM). The XRD diffractograms suggested that only monoborate ions (possibly trigonal and tetrahedral forms) were involved in the intercalation and adsorption. Elemental analyses, i.e. inductive coupled plasma-optical emission and atomic absorption spectroscopies, were used to determine the starting zinc and boron compositions, and the contents after the dissolution experiment in water, soil, and plant growth study. The iZA and cZA samples were found to controlled-release Zn and B contents which can be used as micronutrient sources in agricultural application. The releases of the two nutrients are suggested to initiate from the anionic-exchange of BO33− and the transformation of Zn2+ from LDH basal plane. The plant experiments treated with these iZA and cZA exhibit improvements in plant growth, evidently attributed to the controlled and sustainable releases of boron and zinc for assisting macronutrient uptakes when used with the NPK fertilizer. Boron and zinc are control-released as plant micronutrients via two pathways from synthetic layered double hydroxides. Display omitted •Two forms of ZnAl-LDH with boron association are prepared from ion-exchange process and in-situ co-precipitation.•Trigonal and tetrahedral monoborate ions are intercalated in the LDH interlayer.•Controlled releases of Zn and B are obtained from different processes—Zn transformation to Zn2+ and B ion-exchange process.•Zn and B released from iZA and cZA improve the efficiency of NPK nutrient uptakes in plant.•cZA from co-precipitation method provides more boron that is suitable for the dicot-plant tomato.