A process formes a structure incorporating at least one circuitry transistor and at least one non-volatile memory cell of the EEPROM type with two self-aligned polysilicon levels having a storage transistor and an associated selection transistor in a substrate of semiconductor material including field oxide regions bounding active area regions. The process comprises the steps of in the active area regions, forming a gate oxide layer and defining a tunnel oxide region included in the gate oxide layer depositing and partly defining a first polysilicon layer forming an interpoly dielectric layer and removing the interpoly dielectric layer at least at the circuitry transistor depositing a second polysilicon layer selectively etching away the second polysilicon layer at the cell, and the first and second polysilicon layers at the circuitry transistor and selectively etching away the interpoly dielectric layer and the first polysilicon layer at the cell. After forming and before partially defining the first polysilicon layer, the process implants at least at the channel region of the floating-gate storage transistor for adjusting the transistor threshold.