Agroforestry is an alternative land management system that addresses many of the global challenges, including deforestation, unsustainable cropping practices, loss of biodiversity, increased risk of climate change as well as rising hunger, poverty and malnutrition. It can be an attractive choice for environmental, social and economic development because it does not pollute the environment and can generate additional income to the farmers. In the agroforestry systems, plant residues improve the soil fertility through enhanced nitrogen fixation and maintain microbial activity. Most soils in sub-Saharan Africa are often deficient in nutrients. In the tropics, resource-poor farmers rely on organic inputs to sustain soil fertility. Proper management of crop residues and multipurpose tree prunings can alleviate soil infertility and promote a positive impact on the nutrient dynamics of low-input, maize-banana based agroforestry system in Kisii County. Agroforestry trees are becoming an integral part of agriculture in agroforestry programmes and have been reported to improve soil quality and nutrient cycling. However, intercropping food crops with agroforestry trees may result to competition for resource nutrients. This has not been ascertained in maize-banana based agroforestry systems in Kisii County. Understanding the effect s of intercropping of maize and banana with Sesbania sesban, Calliandra calothyrsus and Leucaena diversifolia agroforestry trees on nutrient dynamics could be a remedy to the problem of nutrient deficiency. The objective of the study was to determine the effect of agroforestry tree species on soil carbon and nutrients (N, P, K, Mg and Ca) in Maize-Banana based agroforestry system. This study was conducted at Kenya Agricultural and Livestock Research Organization farm in Kisii County. The study was carried out on already on-going research which had commenced in March 2018. The experiment was laid out in a Randomized Complete Block Design (RCBD) with maize and banana intercropped with agroforestry trees. Soil samples were collected from the agroforestry fields in Kisii from September, 2018 according to the procedure of Mucheru-Muna [1]. A modified Walkley and Black procedure as described by Zhao et al. [2] was used in the determination of organic carbon. Nitrogen was determined by the Kjeldahl digestion and distillation procedure as described by Bayrakdar et al. [3]. Soil phosphorous, potassium, calcium, magnesium were determined by of Motsara and Roy [4]. Data was subjected to Analysis of Variance and means separated by least significant difference at (p<0.05) using Statistical Analysis Software (SAS). Soils from tree based treatments, Maize, banana and Calliandra calothyrsus, Maize, banana and Leucaena diversifolia and Maize, banana and Sesbania sesban had increased carbon, nitrogen, phosphorus, potassium, calcium and magnesium nutrient levels which increased with time of assessment. In conclusion agroforestry farming system can significantly contribute to provision of carbon and major soil nutrients in Kisii County and the surrounding areas.