Objectives The timing and dietary role of maize agriculture is central to archaeological discussions in the Andean region. In the semi‐arid region of northern Chile (SARNC), archaeological models propose that maize was adopted during the Early Ceramic period in tandem with pottery and sedentism. Through stable isotope (SI) analyses, of bone collagen and apatite, this study assesses the timing of maize introduction, diachronic changes (2,000 BCE to 1,540 CE.), and synchronic dietary variability in the prehistoric SARNC. Materials and Methods Fifty‐two prehistoric individuals from SARNC were analyzed for δ13Cap, δ13Ccol, and δ15N. Descriptive statistics were used to characterize the results by period and location (inland and coast). Between‐periods (ANOVA or Kruskal‐Wallis tests), and synchronic comparisons (inland vs. coast; Student's t‐tests), were conducted. A SIAR model was run to further evaluate dietary changes. Dietary interpretations are based on food web data. Results Coastal groups show significant changes in the diet during the Middle (900‐1,000CE; enrichment in δ13C), and Late Intermediate periods (100‐1450CE; when the Δ13Cap‐col is above 5.2‰). In the inland, significant changes in SI occurred in the Late Intermediate period (δ13C enrichment). In the Late period, the inland diet became enriched for δ15N. Synchronic comparisons showed coastal individuals to have higher δ15N. Discussion The popularization of maize in the SARNC was not associated with the appearance of pottery and/or sedentism, and its role as a dietary staple was a late phenomenon (c.a. 1,000CE). The results obtained in this study show that the adoption and consumption of maize varied dramatically in the Southern Andes.