Uganda Government embarked on promoting sedentary agriculture in Karamoja agro-pastoral semi-arid livelihood zone, which experience rapid environmental and high soil quality (SQ) decline. However, studies on sedentary agriculture’s impact on soil quality using farmer’s knowledge is limited. Consequently, a survey was carried out in Karamoja (Iriiri, Matany Sub-counties of Napak of districts and Rengen sub-county of Kotido) to determine the soil quality indicator parameters based on the farmers knowledge in order to build a local soil knowledge data base to better inform sustainable land use strategies. Using a semi-structured questionnaire, forty indigenous farmers per sub-county, were interviewed between August and September, 2015. The study took into account the social demographic characteristics of the people, farming enterprises, methods of crops production, crops yields trends, causes of the perceived yields trends and soil quality indicators. Prospects of developing Karamoja indigenous knowledge data base lies in visible feature that predict soil quality. Farmers used 36 parameters to determine SQ. The parameters were clustered into five categories; soil, crop, biological, environmental and management each category contributing to 42, 19,14,8 and 17% of the total indicators, respectively. The relationship between age group and the perceived indicators of soil fertility was statistically significant (p-value = 0.045) with the majority stating that they use either soil colour, soil depth or soil texture to express the fertility of soil. The farmer’s soil quality indicators assessed in this study, is important in establishing indigenous-scientific hybrid knowledge data base to enhance soil fertility maintenance and better inform policy makers and other stakeholders on development of sustainable land use strategies.