Crop establishment, determined by shoot and root growth during early growth is a vital component in procuring desired plant populations and high yields in rainfed tropical smallholder farming systems, where green manures help maintain soil fertility and sustainability. As green manure incorporation could affect early seedling growth, studies were conduced in a plant house using soils from fields, to evaluate the impact of incorporating two popular tropical green manures (Crotalaria juncea and Tithonia diversifolia) into soil under rainfed field conditions over 3 years, on selected physico-chemical properties of the soils and on establishment and early shoot and root growth of maize (Zea mays), with and without inorganic fertilizers. In a given year, green manure was grown in one season while maize was grown in the other. A soil that did not receive green manures but was left fallow during the period of green manure cultivation was used as the control treatment. The incorporation of green manures over the 3 years showed trends of increasing soil physical properties, and also the available nitrogen, phosphorus and potassium contents. Incorporation of Crotalaria, with its higher nitrogen content, promoted shoot growth, while Tithonia induced the development of an extended root system. The use of inorganic fertilizers stimulated the beneficial impact of the green manures in promoting shoot and root growth. The use of green manures, especially Tithonia, promoted the development of seminal and nodal roots of maize seedlings, both in the form of length and thickness (based on root surface area) and root length densities, which could assist in successful crop establishment and resource utilization, rather than primary roots. The benefits of using green manures, especially Tithonia, in promoting root growth and Crotalaria in shoot development of maize seedlings even without inorganic fertilizers is presented.