A process for manufacturing deep well junction structures that includes in succession, the steps of: on a first substrate having a first conductivity type and a first doping level, growing an epitaxial layer having the first conductivity type and a second doping level lower than the first doping level; anisotropically etching the epitaxial layer using a mask to form trenches; forming deep conductive regions surrounding the trenches and having a second conductivity type, opposite to the first conductivity type and the second doping level; and filling the trenches. The deep conductive regions are formed by angular ionic implantation and subsequent diffusion of a doping ion species within the epitaxial layer.