This cluster-randomized pragmatic (effectiveness) trial tested maternal counseling based on Motivational Interviewing (MI) as an approach to control caries in indigenous children. Nine Cree communities in Quebec, Canada were randomly allocated to test or control. MI-style counseling was delivered in test communities to mothers during pregnancy and at well-baby visits. Data on outcomes were collected when children were 30 months old. Two hundred seventy-two mothers were recruited from the 5 test and 4 control communities. Baseline characteristics were comparable but not equivalent for both groups. At trial's end, 241 children had follow-up. The primary analysis outcome was enamel caries with substance loss (d2); no statistically significant treatment effect was detected. Prevalence of treated and untreated caries at the d2 level was 76% in controls vs. 65% in test (p = 0.17). Exploratory analyses suggested a substantial preventive effect for untreated decay at or beyond the level of the dentin, d3 (prevalences: 60% controls vs. 35% test), and a particularly large treatment effect when mothers had 4 or more MI-style sessions. Overall, these results provide preliminary evidence that, for these young, indigenous children, an MI-style intervention has an impact on severity of caries (clinical trial registration ISRCTN41467632).