Introduction: The COVID-19 pandemic has had a direct impact on mental health. International organisations have emphasised the vulnerability of indigenous people. Digital Mental Health approaches deliver online therapy as an evidence-based, effective, and accessible treatment option for common mental health problems. However, the evidence regarding these approaches is limited in indigenous populations. The objective of this study is to describe the design, development, and evaluation of the efficacy of a self-applied online intervention regarding the psychological symptoms of depression, anxiety, and fear of COVID-19 in a sample of the Maya population. Method: A prospective longitudinal quantitative study was designed, where a single group was measured before and after receiving the online intervention. This study took place from April to September 2021 and consisted of six sessions delivered via WhatsApp in Spanish and Mayan. Results: The initial assessment was implemented with 82 participants who were evaluated using the Patient Health Questionnaire, Scale for Generalised Anxiety Disorder and the Fear of COVID-19 Scale; 18 participants remained in the intervention for the post-assessment. Statistical differences were observed in PRE and POST measures of depression and anxiety, but not in fear of COVID-19. Conclusions: This study produced positive results for the first online mental health intervention implemented in the Latin American indigenous population. Future studies might consider developing similar interventions for other indigenous communities in Latin America.