In this paper, recent results on the use of low-energy ions in molecular beam epitaxy are described. Mechanisms for ion damage formation are discussed and conditions where ion irradiation can be used without introducing damage are reported. Three main applications are discussed. First, the use of ions to suppress 3D island nucleation during the early stages of strained-layer growth is presented, with particular attention paid to the ion- induced prevention of extended defect formation and strain relaxation. The current understanding of the mechanisms by which ion irradiation affects nucleation is also summarized. Second, ion-induced suppression of phase separation in InGaAsSb alloys during growth on lattice-matched to InP substrates is described. Third, the application of very-low-energy (≈ 50 eV) and glancing-angle 1 keV Ar ions to damage-free sputter cleaning and etching of GaAs is discussed.