The decline of soil fertility status among smallholders is an increasing concern in developing countries like Ethiopia. The purpose of this study was to investigate the soil fertility practices applied by smallholders and current status soil fertility across the agroecological zone of Gedeo zone, Southern Ethiopia. The survey involved 208 randomly sampled smallholder farmers. Soil samples collected from the 108 households and soil fertility indicators such as pH, Total Nitrogen (N), available phosphorus (P), available potassium (K), Soil Organic Carbon (SOC) and Soil Organic Matter (SOM) were analyzed using standard procedures. The result of the study revealed that almost all farmers were dependent on indigenous soil fertility management irrespective of wealth status and agroecological zone. Most of these indigenous practices are organic in nature and highly dependent on local resources. The Soil analysis result revealed that the soil was found to be acidic, clay loam in texture with high SOC, CEC and medium in total N and available P and low in exchangeable K content. The majority of the surface soil (0-30cm) physicochemical properties were significantly affected by agroecological zones but not by wealth status of farmers' households. Based on the result the practices are not sufficiently supplied nutrients to the soil. Hence, to improve the fertility of the soil it is recommended that the application of sufficient organic matter is needed to address soil N, P and K limitations and further studies are needed to integrating indigenous practices with appropriate technologies to maintain soil fertility status.