Investigating COVID-19 transmission and mortality differences between indigenous and non-indigenous populations in Mexico

•Indigenous groups had a 68% higher COVID-19 mortality rate than the non-indigenous groups.•Of 32 federal entities, 23 had a higher mortality rate among the indigenous groups.•The mortality rate ratio and the reproduction number were highest during the fourth wave of the COVID-19 pandemic.•Indigenous populations had a higher care-seeking delay than the non-indigenous populations.•The hazard ratio decreased from 1.67 (unadjusted) to 1.08 in the adjusted model.