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<0.05). However, higher yields were necessary but not sufficient criteria to determine profitability of different treatments. Manure + 60 kg N/ha gave highest NPV (USD 564), Manure + 40kg N/ha gave second highest NPV (USD 511) in Maragwa District while Manure + 60kg N/ha gave highest NPV (USD 633) and Manure + 40kg N/ha second highest NPV (USD 618) in Kirinyaga District. These results suggested that higher N-levels were not necessarily the most economical. Use of organic resources with modest amounts of mineral fertilizers seemed more profitable and held the key to enhancement of nutrient budgets, food security and rural livelihoods.