Calcium leaching is a degradation process consisting in the progressive dissolution of the cement paste as a consequence of the migration of the calcium ions to the aggressive solution. Although the most important changes take place at the nano- and micro-scale, their consequences are observed at every length scale. Within this work, a multi-scale approach combining a wide variety of experimental techniques was used to study such phenomenon in cement pastes with silica nanoparticles. The experimental results proved that the pozzolanic reaction induced by the nanoparticles resulted in a C-S-H gel more stable chemically and with longer silicate chains. In addition, the reduction of the amount of portlandite gave place to pastes with improved microstructure. As a consequence, the performances of such pastes were greatly enhanced both before and during the degradation process.