BACKGROUND: Latin America (LA) has experienced constant economic and political crises that coincide with periods of greater inequality. Between 1996 and 2007 Ecuador went through one of the greatest political and socio-economic crises in Latin America, a product of neo-liberal economic growth strategies. Between 2007 and 2012 it regained political stability, promoted redistributive policies, and initiated greater social spending. To understand the possible influence on the political and economic context, we analyzed the coverage and inequalities in five Reproductive, Maternal, and Child Health (RMNCH) and two water and sanitation interventions using survey data from a broad time window (1994-2012), at a national and subnational level. METHODS: The series cross-sectional study used data from four representative national health surveys (1994, 1999, 2004 and 2012). Coverage of RMNCH and sanitary interventions were stratified by wealth quintiles (as a measure of the socio-economic level), urban-rural residence and the coverage for each province was mapped. Mean difference, Theil index and Variance-weighted least squares regression were calculated to indicate subnational and temporal changes. RESULTS: From 1994 to 2004, Ecuador evidenced large inequalities whose reduction becomes more evident in 2012. Coverage in RMNCH health service-related interventions showed a rather unequal distribution among the socioeconomic status and across provinces in 1994 and 2004, compared to 2012. Sanitary interventions on the contrary, showed the most unequal interventions, and failed to improve or even worsened in several provinces. While there is a temporary improvement also at the subnational level, in 2012 several provinces maintain low levels of coverage. CONCLUSIONS: The remarkable reduction of inequalities in coverage of RMNCH interventions in 2012 clearly coincides with periods of regained political stability, promoted redistributive policies, and greater social spending, different from the former neo-liberal reforms which is consistent with observations made in other Latin American countries. Territorial heterogeneity and great inequalities specially related with sanitation interventions persists. It is necessary to obtain high quality information with sharper geographic desegregation that allows to identify and understand local changes over time. This would help to prioritize intervention strategies, introduce multisectoral policies and investments that support local governments.