A study was conducted in none tilled coffee agroforestry fields of Eastern Uganda to understand the effects of application of inorganic fertilizers on soil nutrient loss in form of gas for mitigation of unsustainable agricultural practices. This study specifically i) assessed the effect of application of inorganic fertilizers on greenhouse gas emissions, ii) determined their effect on microbial carbon, nitrogen and phosphorus and iii) determined their effect on leaf litter decomposition under Albizzia-coffee growing systems of the Mount Elgon. Soil gas emissions were measured with the static chamber method for twelve months in a field experiment with five different fertilizer treatments. The effect of treatments was separated using ANOVA in Genstat discovery version 13. Microbial carbon, nitrogen and phosphorus was separated using Mann-Whitney U test. Results showed that annual emissions ranged from 19.6 to 26.1 (t C/ha/yr), 3.5 to 9 (Kg N/ha/yr) and 6.9 to 9.2 (Kg C/ha/yr) for carbon dioxide, nitrous oxide and methane respectively. Significant effects on soil emissions only occurred for nitrous oxide (P=0.017), microbial carbon (p=0.001) and microbial phosphorus (p<0.001) for the study period. The mixture of NPK fertilizers presented the lowest carbon dioxide loss and application of TSP presented the lowest nitrous oxide emission from soil. This study underscores the need for establishment of long-term experiments across several agro-ecological zones to confirm farmers’ perceptions of their soil fertility levels and ascertain the contribution of farm practices towards the retention of nutrients in the soil with minimal emission, to inform decisions of small holder farmers, policy and development partners for sustainable production.