This study aimed to evaluate two hydrogen peroxide (HP)-based at-home bleaching systems in order to analyze whether nano-hydroxyapatite (nHA) addition may represent a reliable and safe solution for tooth whitening without altering dental microstructure and hardness. Human third molars (N = 15) were treated with two bleaching agents, one containing 6%HP (6HP) and the other 6% HP nHA-enriched (6HP-nHA) with average particle diameter ranging from 5–20 nm. Their effects on enamel were assessed using a spectrophotometer, Vickers microhardness (VMH) test and Scanning Electron Microscopy (SEM), comparing the treated groups with the non-treated control group (CTR). Color analysis revealed improvement in whiteness in both groups compared to CTR. VMH test results showed no differences among the groups. SEM analysis highlighted no evident changes in the enamel microstructure of tested groups compared to CTR. At high magnification, in 6HP group, a slight increase in irregularities of enamel surface morphology was observed, while 6HP-nHA group displayed removal of the aprismatic layer but preservation of the intact prismatic structure. These results suggest that the 6HP-nHA agent may be recommended to provide reliable whitening treatment, without damaging the enamel micromorphology and hardness.