Substance use often begins earlier among American Indians compared to the rest of the United States, a troubling reality that puts Native youth at risk for escalating and problematic use. We need to understand more fully patterns of emergent substance use among young American Indian adolescents, risk factors associated with escalating use trajectories, and protective factors that can be parlayed into robust prevention strategies. We used growth mixture modeling with longitudinal data from middle-school students on a Northern Plains reservation (Wave 1 N = 381, M age at baseline = 12.77, 45.6% female) to identify subgroups exhibiting different trajectories of cigarette, alcohol, and marijuana use. We explored how both risk (e.g., exposure to stressful events, deviant peers) and protective (e.g., positive parent-child relationships, cultural identity) factors were related to these trajectories. For all substances, most youth showed trajectories characterized by low rates of substance use (nonuser classes), but many also showed patterns characterized by high and/or escalating use. Across substances, exposure to stress, early puberty, and deviant peer relationships were associated with the more problematic patterns, while strong relationships with parents and prosocial peers were associated with nonuser classes. Our measures of emergent cultural identity were generally unrelated to substance use trajectory classes among these young adolescents. The findings point to the importance of early substance use prevention programs for American Indian youth that attenuate the impact of exposure to stressful events, redirect peer relationships, and foster positive parent influences. They also point to the need to explore more fully how cultural influences can be captured.