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Ecological sanitation (Ecosan) by-products are inherently limited in their potential use as excreta resources. Disgust behind human excreta and derivatives continues to challenge the further use of Ecosan-by products. Although treated excreta, including Ecosan by-products, have gradually been adopted worldwide, diverse perspectives among users hinder their use in agro-practices. This study explored perceptions of the use of Ecosan-by products as relates to the disgust of human excreta among rural farmers in Burera district, Rwanda. A qualitative study was conducted amongst three farmers' cooperatives using Ecosan by-products. We conducted six focus group discussions (FDGs) comprising a total of 48 participants taking into account the following three themes: core excreta disgust, perceived waste, and perceived resource. Thematic analysis was conducted with similar perspectives identified and grouped under emerging sub-themes. The perspectives regarding disgust elicitors included stigma, eversion, phobia, taboos, and health risks. Ecosan by-products were largely perceived as useful, with most farmers trusting and willing to touch the by-products. Psychosocial barriers to using the by-products continued to slow down the adoption of Ecosan for agricultural options. There is a need for increased awareness to scale up the use of Ecosan coupled with effective treatment practices for the products so as to reverse the psychological barriers resulting from traditional excreta disgust over Ecosan-products of faeces and urine.