The present study utilises dental histological methods to analyse enamel micro‐defects as indicators of early life stress in indigenous Muchik individuals interred at two sites: La Capilla Santa María Magdalena de Eten (CSMME) (n = 15) and La Capilla del Niño Serranito (CNS) (n = 15), both located in the Lambayeque Valley region of northern Peru. Individuals interred at CNS date to the Early Colonial Period (AD 1533–1610), and individuals interred at CSMME date to the Middle/Late Colonial Period (AD 1625–1760), thus permitting comparison of childhood stress events between the Early and Middle/Late Colonial Periods. Results reveal a high prevalence of Wilson bands at both sites, although a lower prevalence at the CSMME was observed in comparison with the CNS. This indicates that, over time, Muchik individuals in this town may have been able to acclimate to life under Spanish oppression. Stress chronologies suggest that early life stress possibly resulted from inadequate and less than desirable food and/or water available for supplemental feeding during early infancy, especially around the ages of 4 and 5 months. Furthermore, results show that individuals with enamel defects in the form of Wilson bands at both the CNS and CSMME had an earlier mean age‐at‐death (9.6 and 4.05 years, respectively) in comparison with those without observed Wilson bands (19.75 and 8.8 years, respectively). These results underscore the importance of not only regional and temporal studies of the biological consequences of Spanish contact in the Americas but also of investigating the relationship between early life stress and adult health and longevity in archaeological populations. Copyright © 2015 John Wiley & Sons, Ltd.