A study of Zn1-xMnxO (x=0.02 and 0.04) pellets synthesized by sol-gel technique was performed to explore the inherent magnetic interactions. 50MeV Li3+ ion beam irradiation was employed to a Zn0.96Mn0.04O pellet. Structural, morphological, compositional and magnetic properties of the samples were investigated. The single-phase structural nature was destroyed for a 4 at% Mn-doped sample with the formation instead of a new phase of ZnMnO3, as observed from the X-ray diffraction (XRD) pattern. The intensity of the multiphase component decreases with the ion irradiation. XRD also indicates that Mn incorporation in ZnO increased with increasing doping and, interestingly, with irradiation. The tendency of grain size is the opposite. The magnetic measurements of the samples indicate anti-ferromagnetic interactions coupled with paramagnetic counterparts. The study clearly exhibits the modification of magnetic properties with Li3+ ion beam irradiation. It has been interpreted that structural and compositional quality up-gradation with irradiation is responsible for such changes in magnetic behavior. © 2011 Taylor & Francis.