Climate change, land degradation and inadequate soil nutrients pose significant threats to food security and agricultural sustainability. This study aims to examine the effects of planting basins with farmyard manure on soil total carbon (C), nitrogen (N), isotopic C (δ13C) and N (δ15N) compositions within smallholder-managed farms in Makueni County, Kenya. The study involved two management practices: planting basins with manure (PM) and conventional farming practices (FP) in 12 experimental sites. Soil samples were taken at three depths (0–10, 10–20 and 20–40 cm), with three replicates for each treatment. Significant interactions were observed between land management practices and sites as well as land management practices and soil depth on soil total C and N. At each of the 12 sites, soil total C was higher under PM (ranging from 0.44% to 1.86%, p <.05) than FP management (ranging from 0.35% to 1.37%), across all soil depths. Soil total N concentrations ranged from 0.027% to 0.100% under FP and (0.060% to 0.190%, p <.05) under PM management. Across soil depths, higher (less negative) soil δ13C values were observed under conventional farmer practice (range − 22.5‰ to −17.1‰) compared with PM management range (−24.3‰ to −18.1‰). Soil δ15N was significantly enriched under PM management (range: 7.4‰ to 12.6‰, p <.05) compared with the conventional farmer practices (range: 6.1‰ to 9.8‰, p <.05). The findings show that planting basins with farmyard manure offers both climate mitigation and adaptation benefits by increasing soil C contents and improving soil fertility. The study provides insights into the real-world implications of these practices, emphasizing the potential of planting basins with manure in enhancing soil quality and climate resilience.