Ecological sanitation (Ecosan) is a relatively new concept being promoted in many developing countries to improve sanitation coverage and recycle nutrients in excreta for agricultural production. We conducted a cross-sectional study in Kabale municipality, western Uganda to determine the coverage of Ecosan and factors affecting its uptake. A total of 806 respondents were interviewed, randomly selected from 32 of 77 (42%) villages in Kabale municipality. We held six focus group discussions and 10 key informant interviews. Ecosan coverage was found to be 20% (163/806). The factors that were significantly associated with Ecosan coverage included education, occupation, religion and age. Our study found a relatively high Ecosan coverage in Kabale municipality compared to the targeted national coverage of 15% by 2018. Policy-makers and organizations in Ecosan development ought to take into consideration the influence of education and socio-economic factors for successful uptake of ecological sanitation.