Background: Few studies have examined the development of geographic and socioeconomic inequalities in caries over time or have simultaneously assessed individual-level socioeconomic position (SEP) and neighborhood-level factors as a multi-layered phenomenon influencing caries inequalities. This study examined (i) the trends in geographic inequalities in caries among adolescents in Denmark and (ii) how the association between SEP and caries has progressed over time, when accounting for individual and neighborhood-level confounding factors. Methods: This nationwide repeated cross-sectional study included 15-year-olds in Denmark from 1995, 2003, and 2013 (n = 149,808). The outcome was caries experience (measured by the decayed, missing, and filled tooth surfaces [DMFS] index). The exposure of interest was SEP, indicated by the previous year’s parental education, occupational social class, and (equivalized) disposable household income. Covariates included individual-level factors (immigration status, country of origin, number of children and persons in the family, and household type) and neighborhood (residence municipality)-level factors (Gini index; proportion of unemployed, low-educated, and unmarried/non-cohabiting individuals; proportion of single-parent households and households with overcrowding). Data sources included the Danish national dental and administrative social registers and Statistics Denmark’s statistics database (StatBank). Data were analyzed using spatial and spatiotemporal modelling utilizing zero-inflated negative binomial regressions and integrated nested Laplace approximations for Bayesian parametric inference. Observed caries experience geo-maps of the Danish municipalities for 1995, 2003, and 2013 were created. Results: Between 1995 and 2013, caries prevalence in the 15-year-olds declined sharply (1995, 71%; 2013, 45%). Caries experience declined in nearly all socioeconomic subgroups and municipalities. However, geographic inequalities persisted with higher caries levels largely concentrated in the relatively deprived areas of Denmark. Increasing relative socioeconomic inequalities in caries over time were observed with significant graded associations between SEP and caries despite adjustment for the various individual and neighborhood-level covariates and the effect of assessment year (e.g., 15-year-olds with parents having basic education had 1.91-fold [95% CI: 1.86–1.95] higher caries experience than those having parents with high education). Conclusions: Reducing these enduring inequalities will likely require additional resources and targeted supportive and preventive measures for adolescents from lower SEP backgrounds and those residing in municipalities with higher caries prevalence.