In this work, we present evidence that Be3P2 microcrystals are formed in Be-doped phosphorus-based semiconductor compounds grown by chemical beam epitaxy. Our results suggest that microcrystal formation occurs when high Be concentrations (>1018 cm−3) and temperatures higher than 500 °C are used for crystal growth. The main consequence of Be3P2 formation is a high phosphorus consumption close to these microcrystals that causes a large density of P vacancies in the semiconductor layer. This results in reduced electrical mobility, lattice parameter reduction, and poor crystalinity of the film in general.