This paper examines three different soil fertility management practices and their effect on the soil quality in smallholder farming systems in the Kenyan Highlands. Soil organic matter (SOM) is greatly affected by how the soil is managed and treated. When testing humic nitisol (Kikuyu Red Clay) under a maize-bean rotation, it was found that the management practice of retaining the maize stover and adding manure produced the best results. Fertilization and crop residue removal resulted in the greatest decline in SOM. This research shows that effective soil management practices are important to soil quality and crop production in this area of Kenya.