The development of self-healing materials, based on polymer blends, is an important issue either from a scientific or a technological point of view. The application of such materials can be remarkably extended if healing effects can be maintained even in polymers that are modified in order to tune their physical and mechanical behavior. In this research the self-healing behavior of blends made of ionomers (sodium and zinc salts of poly(ethyelene-co-methacrylic acid)—EMNa and EMZn) with functionalized elastomers (epoxidized natural rubber with different epoxidation levels—ENR50 and ENR25, polyisoprene—PISP) of different compositions is investigated. The role of processing conditions, phase morphology, functionalization level, polymers compatibility over self-healing response are discussed. Rubber functionality and phase dispersion are recognized as crucial factors affecting the healing efficiency of blends. Results of ballistic tests, DSC thermal analysis, FTIR spectroscopy, optical and electron (SEM and TEM) microscopy observations, rheological and mechanical tests are presented as supporting evidences.