In Kisumu up to 60% of the inhabitants practice some form of urban agriculture, with just under 50% of the workers being female. On average, women spend more hours a day in the gardens than men. Therefore women's knowledge is pivotal for effective agricultural management. To enhance and better use women's knowledge, gender-related sociocultural obstacles linked to land ownership, investment, and farm inputs have to be taken into account. We aimed to determine how the agricultural knowledge and motivations of female farmers working in the Nyalenda urban gardens in Kisumu (Kenya) influence the soil nutrient status as reflected by the total soil C and N; available soil N and P; and exchangeable soil Na, K, Mg, and Ca. Two prevailing practices were compared to determine how the agricultural management practice influences soil nutrient content: (1) applying manure only and (2) applying manure while intercropping with cowpeas. Interviews and focus group discussions were held to explore the agricultural knowledge and motivations of the women working in Nyalenda. Soil analysis showed that the soil in Nyalenda was rich in nutrients overall but that the intercropped fields contained significantly lower total soil nutrients than fields where only manure was applied. While theoretically intercropping with a legume such as cowpeas should increase soil N content, due to socioeconomic factors, such as poverty, intercropping was applied in a way that did not increase soil nutrient contents; rather it diversified revenue. The knowledge of the female farmers was found to be limited to practical and sensory knowledge. This shows that when aiming to improve soil nutrient status and agricultural yields through agricultural training, socioeconomic conditions, cultural context, and gendered knowledge differentiation have to be acknowledged.