Due to its unique properties, zirconia is increasingly being used in dentistry, but surface preparation for bonding is difficult because of its polycrystalline structure. This study aimed to determine the effect of a new etching technique (Zircos-E) on Ceramill Zi (Amann Girrbach). The effect of etching and the use of primers (Monobond Plus and MKZ Primer) on the bond strength of zirconia with resin cement (NX3) was assessed. Shear bond strength was evaluated after storage in water for 24 h and after thermal aging (5000 thermocycling at 5 °C/55 °C). A scanning electron microscope (Hitachi S-4700) was used to evaluate the surface structure before and after the Zircos-E system. The roughness parameters were assessed using an SJ-410 profilometer. The etched zirconia surface is more homogeneous over the entire surface, but some localized forms of erosion exist. The etching of zirconia ceramics caused changes in the surface structure of zirconia and a significant increase in the shear bond strength between zirconia and resin cement. The use of primers positively affects the adhesion between resin cement and zirconia. Aging with thermocycler significantly reduced the shear bond strength, with one exception—sandblasted samples with MKZ Primer. Standard ceramic surface preparation, involving only alumina sandblasting, does not provide a satisfactory bond. The use of etching with the Zircos-E system and primers had a positive effect on the strength of the zirconium–resin cement connection.