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Structural adjustments programs (SAPs) in the last two decades have eliminated all farm-support programs leading to low usage of fertilizers by Kenyan smallholders. One way of addressing this problem is use of organic nutrient resources. This paper examines their cost-effectiveness as capital investments in replenishment of Nitrogen (N), Phosphorus (P), Potassium (K) and soil organic matter (SOM) in smallholder, Maize-based cropping systems. On-farm trials were established in Maragwa and Kirinyaga Districts in 2003/04. Maize was planted in 3 replicates in randomised complete block design (RCBD) using different levels of organic and inorganic fertilizer resources. A blanket rate of 40kg P/ha was applied in all treatment except the control to increase organic N-utilization efficiency. The test crop was harvested, oven-dried and weighed. Net Present Values (NPV) were computed using Partial Budgeting Analysis Model. Increasing levels of inorganic N increased maize yields significantly (P