In this research, the effect of the addition of zirconium oxide-synthesized nanoparticles on the microstructural development and the physical–mechanical properties of cement mortars with limestone aggregates was studied. Zirconia nanoparticles were synthesized using the co-precipitation method. According to XRD analysis, a mixture of tetragonal (t) and monoclinic (m) zirconia phases was obtained, with average crystallite sizes around 15.18 and 17.79 nm, respectively. Based on the ASTM standards, a mixture design was obtained for a coating mortar with a final sand/cement ratio of 1:2.78 and a water/cement ratio of 0.58. Control mortars and mortars with ZrO2 additions were analyzed for two stages of curing of the mortar—7 and 28 days. According to SEM analysis, mortars with ZrO2 revealed a microstructure with a high compaction degree and an increase in compressive strength of 9% on the control mortars. Due to the aggregates’ characteristics, adherence with the cement paste in the interface zone was increased. It is suggested that the reinforcing effect of ZrO2 on the mortars was caused by the effect of nucleation sites in the main phase C–S–H and the inhibition of the growth of large CH crystals, and the filler effect generated by the nanometric size of the particles. This produced a greater compaction volume, suggesting that faults are probably originated in the aggregates.