Purpose <p>The aim was to compare the prevalence of molar incisor hypomineralisation (MIH) obtained from two cross-sectional surveys conducted in 2018 and 2023 and to evaluate their association with other variables in schoolchildren attending elementary schools in Tepatitlán de Morelos (Jalisco, Mexico).</p> Methods <p>Children (5–13&#xa0;years old) enrolled in elementary schools in Tepatitlán de Morelos, Mexico, were evaluated. Intra-oral examinations were performed in schools by calibrated examiners. In both surveys, the presence and characteristics (including severity) of MIH and hypomineralised second primary molars (HSPM) were scored according to the European Academy of Paediatric Dentistry (EAPD) MIH-index. In 2023, dental plaque and dental caries were scored additionally. Descriptive and statistical analyses were performed (<i>α</i> = 5%, 95%&#xa0;CI).</p> Results <p>In total, 959 schoolchildren were evaluated; MIH prevalence was 35.78% in 2018 and 26.58% in 2023 (<i>p</i> = 0.002). Tooth-level prevalence of MIH decreased significantly from 12.71% to 8% when comparing the two surveys (<i>p</i> &lt; 0.001). Higher prevalence of HSPM was observed in children with MIH, compared to children without MIH in both surveys (<i>p</i> &lt; 0.001). Neither the number of teeth presenting cavitated caries lesions (<i>p</i> = 0.193), nor the plaque score (<i>p</i> = 0.061) was associated with the presence of MIH in 2023. Children with severe MIH had a higher likelihood to have cavitated caries lesions compared to children with mild MIH (<i>p</i> = 0.001).</p> Conclusion <p>A statistically significant decrease in the MIH prevalence was determined at both child and tooth level in the period 2018–2023.</p>