Mortality registries are an essential data source for public health surveillance and for planning and evaluating public policy. Nevertheless, there are still large inequalities in the completeness and quality of mortality registries between and within countries. In Ecuador, there have been few nationwide evaluations of the mortality registry and no evaluations of inequalities between provinces. This kind of analysis is fundamental for strengthening the vital statistics system. Ecological study assessing the completeness, quality and internal consistency of mortality data in the provinces of Ecuador, using 13 years of mortality data (2001-2013). Completeness was assessed using three types of death distribution methods (DDMs), quality by estimating the percentages of garbage codes and deaths with unspecified age or sex in the registered deaths, and internal consistency by estimating the percentage of deaths with reported causes of deaths considered impossible in some age-sex combinations. Finally, we propose a classification of the mortality registry in the studied areas based on completeness and quality. Completeness estimates (mean of the three methods used) in the provinces ranged from 21 to 87% in women and from 35 to 89% in men. The percentage of garbage codes in the provinces ranged from 21 to 56% in women and from 25 to 52% in men. Garbage coding was higher in women and in older age groups. The percentage of deaths with unspecified age or sex, and the percentage of deaths with reported causes of deaths considered impossible in some age-sex combinations was low in all the studied areas. The mortality registry could only be classified as acceptable in one area for men and one area for women. We found substantial inequalities by sex, geographical areas and age in the completeness and quality of the mortality registry of Ecuador. The findings of this study will be helpful to direct measures to improve Ecuador's vital statistics system and to generate strategies to reduce bias when using mortality data to analyse health inequalities in the country. The online version of this article (10.1186/s12963-019-0183-y) contains supplementary material, which is available to authorized users.