The layered structure of MAX phases is associated with a number of functional properties and is the subject of extensive research. While the unit-cell layers of these structures have been well studied, much less is known about the distribution and manipulation of point defects within them. Here, we selected the prototype Cr₂AlC system and, using variable energy positron beams, observed Doppler broadening and positron annihilation lifetimes to track the evolution of defects caused by the penetration of energetic transition metal ions (Co⁺ and Mn⁺) and noble gas ions (Ar⁺ and Ne⁺). In all cases an overall reduction of the open-volume defect concentration is observed post-irradiation. Atomic displacements induced by the penetrating ions drastically modify the defect distribution: the concentration of agglomerates of 9–15 vacancies (corresponding to positron lifetimes of 335–450 ps) in the precursor [Cr₂C/Al]n layers is suppressed, whereas Al mono- and Al-Cr di-vacancy (lifetimes 217–231 ps) concentrations are enhanced. This breakdown of large defects into point defects scales with atomic displacements and is largely independent of the penetrating ion species, providing insights into the manipulation of point defects in nano-layered systems.