In this work, we study ultra-low energy implantation into MoS2 monolayers to evaluate the potential of the technique in two-dimensional materials technology. We use 80Se+ ions at the energy of 20 eV and with fluences up to 5.0·1014 cm−2. Raman spectra of the implanted films show that the implanted ions are predominantly incorporated at the sulfur sites and MoS2−2xSe2x alloys are formed, indicating high ion retention rates, in agreement with the predictions of molecular dynamics simulations of Se ion irradiation on MoS2 monolayers. We found that the ion retention rate is improved when implantation is performed at an elevated temperature of the target monolayers. Photoluminescence spectra reveal the presence of defects, which are mostly removed by post-implantation annealing at 200 °C, suggesting that, in addition to the Se atoms in the substitutional positions, weakly bound Se adatoms are the most common defects introduced by implantation at this ion energy.