Awareness of how soil properties vary over agroecosystems (AES) is essential for understanding soil potentials and improving site-specific agricultural management strategies for a sustainable ecosystem. This study examined the characteristics of soil quality attributes and implications for agriculture in the Choke Mountain watershed in Ethiopia. Forty-seven composite soil samples (0–20 cm deep) were collected from lowland and valley fragmented (AES 1), midland plain with black soil (AES 2), midland plain with brown soil (AES 3), sloppy midland land (AES 4), and hilly and mountainous highlands (AES 5). Ten of 15 soil quality properties were significant (P < 0.05 or 0.01), including silt, exchangeable bases, cation exchange capacity, percent base saturation, pH, organic matter, total nitrogen and available phosphorous (P) across the five AES. However, all properties were variable with coefficients of variation from 7% (total porosity) to 169% (available P) across the AES. Although AES 2 and 3 are affected by waterlogging and acidity, these two have better prospects for agriculture, but AES 1, 4, and 5 are unsuitable for agriculture because of soil erosion. Therefore, appropriate and applicable soil management strategies, particularly lime application and organic fertilizer, are fundamental to reversing soil acidity and improving soil fertility.