A 3D CFD model of the agglomeration of droplets and particles in a counter-current spray drying process was developed and verified. An original discrete phase model was elaborated, with an agglomeration module taking into account hydrodynamic segregation of particles, droplet coalescence and droplet shrinkage, for accurate calculations of mass balance of the discrete phase. The characteristic drying curves were applied to the model of particle moisture evaporation, which included the coupling of particle agglomeration with heat, mass and momentum transfer between the discrete and continuous phases. Two agglomeration zones were observed in the tower: wet particle agglomeration in the atomization zone, and "dry agglomeration" above the air inlets, due to the intensive mixing of particle streams. A comparison of the calculated particle size distributions and experimental data obtained from particle dynamics analysis (PDA) measurements proves the accuracy of the developed methodology. The elaborated model allows the final PSD of the powder in the spray towers to be predicted.