Irradiation with high-energy ions has been widely suggested as a tool to engineer properties of graphene. Experiments show that it indeed has a strong effect on graphene's transport, magnetic and mechanical characteristics. However, to use ion irradiation as an engineering tool requires understanding of the type and detailed characteristics of the produced defects which is still lacking, as the use of high-resolution transmission microscopy (HRTEM) -the only technique allowing direct imaging of atomic-scale defects -often modifies or even creates defects during imaging, thus making it impossible to determine the intrinsic atomic structure.Here we show that encapsulating the studied graphene sample between two other (protective) graphene sheets allows non-invasive HRTEM imaging and reliable identification of atomicscale defects. Using this simple technique, we demonstrate that proton irradiation of graphene produces reconstructed monovacancies, which explains the profound effect that such defects have on graphene's magnetic and transport properties. This finding resolves the existing uncertainty with regard to the effect of ion irradiation on the electronic structure of graphene.Knowing the detailed microscopic structure of atomic-scale defects in graphene, such as vacancies or grain boundaries, is crucially important for understanding and potentially controlling their effect on electronic and spin transport, mechanical strength, chemical reactivity and thermal conductivity of