The interaction of plasma with materials is critical for the fundamental understanding of non-equilibrium processes and their wide application. Recent achievements in fusion energy research emphasize the importance of this problem. Because modelling and predicting plasma–material interactions (PMI) require considering a tremendous number of single plasma particle–surface interaction events, this type of modelling was, until recently, possible only within a binary collision approximation (BCA). The BCA approach considers materials as uniform temperature-insensitive media. The research presented here addresses the PMI problem within an atomistic-based approach for the first time at a statistically significant level. Approximately 105 molecular dynamics trajectories were generated for 100 eV deuterium ions interacting with a tungsten surface. The research demonstrated the critical importance of incorporating the discrete lattice structure of matter into the model. Deuterium penetration depth and fraction of backscattered deuterium ions strongly depend on the surface orientation, the impact incident ion directions, and the ions’ initial positions. On average, the BCA-based calculations underestimate the penetration depth by a factor of two or more, and the fraction of backscattered atoms is overestimated by a factor of two or more. Furthermore, increasing the material temperature from 500 to 3000 K reduces penetration depth by about 30% and increases the fraction of backscattered atoms by 250%.