Purpose: Soil quality is critical for plant growth and ecosystem sustainability. Understanding the indicators that indicate soil quality is, therefore, crucial. Labile organic carbon (C) and nitrogen (N) are important components of soil functions that impact productivity and environmental stability. This study aimed to explore the sensitivity of different labile C and N fractions, including water extractable organic C (WEOC) and total N (WEON) and hot water extractable organic C (HWEOC) and total N (HWEON), to planting basins with manure compared to conventional farming practices. Methods and methods: Soil samples were drawn from 0–10 and 10–20 cm soil depths at 12 sites in Makueni County, Kenya. Samples were analysed for differences in WEOC, HWEOC, WEON, and HWEON between planting basins with manure and conventional farmer practices. We also assessed the correlations of the different labile C and N pools with other soil chemical properties linked to soil quality. Results and discussions: The results showed that planting basins with manure significantly increased mean WEOC (171.53 µg g−1), HWEOC (353.62 µg g−1), WEON (26.60 µg g−1), and HWEON (26.39 µg g−1) compared to those of conventional farming practices (p < 0.05). WEOC was positively correlated with WEON and δ15N (p < 0.001) at the 0–10 cm soil layer suggesting that extractable organic matter can be used as an index for soil health and nutrient content. Conclusion: The findings suggest that cold water and hot water extractable C and N are sensitive indicators of the effects of different land management practices on soil quality. The results further demonstrate that planting basins with manure can improve soil quality by increasing labile C and N pools.