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Ion irradiation is a versatile tool to introduce controlled defects into two-dimensional (2D) MoS₂on account of its unique spatial resolution and plethora of ion types and energies available. In order to fully realise the potential of this technique, a holistic understanding of ion-induced defect production in 2D MoS₂crystals of different thicknesses is mandatory. X-ray photoelectron spectroscopy, electron diffraction and Raman spectroscopy show that thinner MoS₂crystals are more susceptible to radiation damage caused by 225 keV Xe⁺ions. However, the rate of defect production in quadrilayer and bulk crystals is not significantly different under our experimental conditions. The rate at which S atoms are sputtered as a function of radiation exposure is considerably higher for monolayer MoS₂, compared to bulk crystals, leading to MoO₃formation. P-doping of MoS₂is observed and attributed to the acceptor states introduced by vacancies and charge transfer interactions with adsorbed species. Moreover, the out-of-plane vibrational properties of irradiated MoS₂crystals are shown to be strongly thickness-dependent: in mono- and bilayer MoS₂, the confinement of phonons by defects results in a blueshift of the$A_{1g}$mode. Whereas, a redshift is observed in bulk crystals due to attenuation of the effective restoring forces acting on S atoms caused by vacancies in adjacent MoS₂layers. Consequently, the$A_{1g}$frequency of tri- and quadrilayer crystals is statistically invariant on account oft competition between phonon confinement effects and interlayer interactions. The$A_{1g}$linewidth is observed to decrease in bi- and trilayer crystals after low dose irradiation and is attributed to layer decoupling. This work shows that there is a complex interplay between defect production, crystal thickness and interlayer interactions in MoS₂. Our results demonstrate that ion irradiation is an effective tool to modulate the electronic, vibrational and structural properties of MoS₂, which may prove beneficial for practical applications.