A perpendicularly magnetized magnetic tunnel junction (p-MTJ) is disclosed wherein a boron containing free layer (FL) is subjected to a plasma treatment with inert gas, and a natural oxidation (NOX) process to form B2O3 before overlying layers are deposited. A metal layer such as Mg is deposited on the FL as a first step in forming a Hk enhancing layer that increases FL perpendicular magnetic anisotropy, or as a first step in forming a tunnel barrier layer on the FL. One or more anneal steps are essential in assisting B2O3 segregation from the free layer and thereby increasing the FL magnetic moment. A post-oxidation plasma treatment may also be used to partially remove B2O3 proximate to the FL top surface before the metal layer is deposited. Both plasma treatments use low power (