Early-life intervention to reduce obesity and poor dental health through early-life nutrition will improve health outcomes in later life. This study examined the prevalence of overweight and obesity and visual dental decay in 4-year old children in New Zealand between 2013 and 2017, and the impact of a nutrition and physical activity intervention programme, Under-5-Energize (U5E), on prevalence of these conditions within ethnic groups and by deprivation. The data set included 277,963 4-year-old children, including 25,140 from the Waikato region children of whom 8067 attended one of the 121 early childhood centres (ECC) receiving the U5E programme from 2014. Purposively the U5E-ECC selected were attended by higher proportions of indigenous Māori children and children living in higher deprivation areas than non-U5E-ECC. From 2013 to 2017, the overall prevalence of obesity, as defined by World Health Organisation criteria, declined slightly but rates of dental decay did not change. In the Waikato region, the prevalence of obesity declined in non-Māori children from 2015 to 2017 and children attending U5E-ECC had lower rates of dental decay than non-U5E children. Binary logistic regression showed that between 2015 and 2017 visible dental decay was more likely in children who were Māori (3.06×3.17), living in high deprivation (1.54×1.66) and male (1.10) but less likely if attending an U5E-ECC (0.83×0.79). Early-life intervention had efficacy at reducing dental decay, and demonstrated that the origins of disparities in health such as ethnicity and deprivation need to be addressed further to break the intergenerational cycles of poor health.