Efforts to improve soil productive capacity aimed at boosting crop production in the Northern Ghana has primarily focused on field-based experiments with little documentation on farmer practice and local indigenous knowledge of soil management. A sample group of 114 farmers from five farming communities in the Guinea Savannah was interviewed to evaluate their indigenous knowledge of crop production practices in the context of soil health, fertilization management, and crop yield. Data were collected using semi-structured interviews and responses for each category were calculated using simple proportions. Farmers’ fertilization practice was primarily influenced by fertilization resource availability and crop yield response. The results showed that inorganic fertilization was the commonest fertilization type among farmers. Farmer local indicators of soil health were predominantly limited to visually observable signs such as presence or absence of indicator plants, growth vigor of plants, soil color, and tilth, texture, and compaction. Non-tactile and visible indicators, notably soil chemical composition and presence of soil microorganisms, was rarely used. The listed indicators were congruent with scientific reports, although some knowledge gaps, particularly on the use of indicator plants, were identified. The use of indicator plants as determinants of healthy or non-healthy soils appeared to be influenced by the ease of control of weeds, its utilitarian benefits, benefits to the soil, and threats on cultivated crops. Famers were well informed about the decreasing crop yield. Fertilization practices and limitations in soil management practices with proposed capacity building approaches aimed at enhancing productive capacities of cultivated farmlands are discussed.