Background: Best practices in breastfeeding are often not followed despite appropriate levels of knowledge and positive attitudes regarding the benefits of human milk. For many reasons, some women do not initiate breastfeeding, suspend breastfeeding early, or initiate complementary feeding earlier than recommended. Usual measurement methods use large sample surveys at a national scale, which are not well suited for monitoring sub-national differences. Methods: In order to understand how local infant feeding practices could influence policy and promotion practices, we apply data pooling methodology to analyse breastfeeding patterns in different Ecuadorian settings: Cumbayá parish, located near Quito, the Ecuadorian capital; the city of Macas and rural surroundings in the Amazon basin province of Morona Santiago; and the province of Galapagos. Surveys were conducted independently between August 2017 and August 2018; while they are representative of each respective setting, sampling designs and survey methods differ, but the same demographic information and data based on standard breastfeeding indicators established by the World Health Organization (WHO) were collected. In order to account for differences in the different settings, the design effect of each survey was considered in the analysis. Results: Significant differences were found in breastfeeding practices between the suburban Cumbayá parish near Quito and Galapagos on one hand, and urban and rural parts of Morona Santiago, on the other. The rates of early breastfeeding initiation and age-appropriate breastfeeding are significantly higher in urban and rural Morona Santiago then in Cumbayá or Galapagos, while the rate of exclusive breastfeeding is highest in rural parts of Morona Santiago. No significant differences were found in complementary feeding practices between Cumbayá and Galapagos, but there are with urban and rural Morona Santiago. Initiation of breastfeeding in the first hour after birth occurs in only 36.2% of cases in Cumbayá but in 75.4% of cases in urban Morona. Conclusions: Differences among regions reflect specific opportunities and barriers to practices related to promoting optimal infant health and nutrition. Consequently, regional or local conditions that often are not apparent in national-level data should orient policies and promotion activities in specific populations.