This work presents the first results of synthesis of framework binary phosphates of zirconium and transition metal cations (Co, Cu, Ce) via nanocomposites of starting inorganic salts with citric acid and studies of their structure genesis. Nanoparticles of layered Zr phosphates with typical sizes in the range of 18–24 Å are formedat the mixing stage. Less basic Cu and Co cations are mainly octa-coordinated with both phosphate groups of those nanoparticles and citric acid molecules. At subsequent thermal treatment, Cu and Co cations are incorporated within Zr phosphate nanoparticles acquiring a low coordination approaching a tetrahedral one while rearranging the nuclei structure into that of a framework type. Removal of citric acid by heating under air at 200–300°C preserves the size of nanoparticles while their ordered stacking forms mesoporous structure with a narrow pore size distribution ∼ 50 Å and specific surface area up to 200 m2/g after calcination at 600°C. The binary phosphates promoted by a small amount of Pt were found to be effective catalysts of NOx selective reduction by decane in the oxygen excess not subjected to coking with a high and stable performance at high space velocities in the presence of steam.