ObjectivesThe aim of this randomized clinical trial was to evaluate the desensitizing and remineralizing effect of a new zinc‐hydroxyapatite‐based paste in sites affected by molar–incisor hypomineralization (MIH), by assessing dental sensitivity, tooth wear, and periodontal indexes.Materials and MethodsTwenty‐five patients with presence of 1 enamel demineralization of permanent molars and incisors in two different quadrants were recruited. After professional dental hygiene, a domiciliary hydroxyapatite‐based paste was assigned and recommended to be applied on 2 MIH teeth in one random quadrant (test group), while the 2 contralateral MIH teeth did not undergo paste application (control group). The following primary outcomes were assessed: Plaque Control Record (PCR), Bleeding Index (BI), MIH Treatment Need Index (MIH‐TNI), and Schiff Air Index (SAI).ResultsNo significant inter‐ and intragroup differences were found for PI and BI, except for both intragroup T0–T1. For MIH‐TNI, significant intergroup differences were detectable in the test group after 9 months of treatment. For SAI values, no significant differences were found in the control group, while in the test group, significant lower values were found after 1 and 3 months since baseline, respectively.Conclusions and Clinical RelevanceBiomimetic zinc‐hydroxyapatite showed a desensitizing effect when used to treat MIH.