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Background/Objectives: Indigenous children in La Guajira, Colombia, live in a context of structural vulnerability that may compromise growth and nutritional status. This study aimed to characterize anthropometric patterns and longitudinal nutritional changes in Wayúu children under five years of age. Methods: We conducted a prospective cohort study in 398 children from 27 Wayúu communities in Manaure, La Guajira, over an 8-month period. Anthropometric measurements were obtained by pediatricians and classified using standard indicators based on WHO growth references. A descriptive and bivariate analysis was performed for the full sample, and longitudinal changes were evaluated in a follow-up subgroup. Results: At baseline, 92.46% of children presented at least one nutritional alteration, and 89.95% had malnutrition or developmental delay. Stunting was the most frequent condition (89.95%), whereas acute malnutrition was less common. In the longitudinal subgroup, 41.67% of children worsened in at least one indicator, with a significant increase in nutritional risk over time. Older children showed worse weight-for-age and height-for-age indicators than younger children, while no significant differences were observed by sex. Conclusions: Wayúu children under five years in Manaure show a pattern dominated by chronic, symmetrical growth impairment with worsening anthropometric trajectories over time. These findings highlight the need for sustained, culturally adapted, and multisectoral strategies to prevent and manage childhood malnutrition in Indigenous populations.