The analysis of health phenomena among the indigenous population often fails to acknowledge diversity and contextuality, leading to portrays that homogeneize ethnic groups. In the case of the Covid-19 vaccination in Mexico, recent studies highlight that “indigenous language speakers showed a lower vaccination rate” and were “more likely to cite negative beliefs about the vaccine” (Abascal Miguel et al. 2024). With the intention of providing a context-based analysis of Covid-19 vaccination uptake or refusal, we carried out a mixed-methods research (ethnography and health data exploratory statistical analysis) in two nearby Zapotec communities in Oaxaca, southern Mexico. Despite geographical, demographic, and cultural similarities, these two communities presented differences in Covid-19 acceptance. In this presentation, we share some preliminary research results and hypothesize the sociocultural, political, and organizational factors at community and governmental levels that might have influenced the divergent outcomes of the vaccination campaigns. We conclude by calling for an integration of micro and macro-level analysis in order to gain a nuanced and complex understanding of health processes among indigenous populations. This kind of approach can offer culturally and socially grounded information to better device health policy.