Alternate wetting and drying irrigation (AWD) is promulgated as a practice for reducing irrigation water usage in rice production; however, the implications of AWD on soil properties and crop growth remain unclear. Here, we conducted a global meta-analysis encompassing 3194 observations from 200 published studies to assess the systemic effects of AWD on the aforementioned indices with the explicit aim of identifying approaches for yield improvement in rice. The results showed that, compared with continuous flooding, AWD increased water use efficiency by 31% but with an average yield penalty of 6%. Optimal AWD was applied when water potential was maintained at pressures greater than −15 kPa with water depths less than 18.5 cm during rice growing season. Changes in total organic carbon (TOC), pH and nitrate-nitrogen (NO₃⁻) in soil had significant influence on yield. These analyses suggested that limiting the effect sizes of TOC to less than 0.0003, pH above −0.015 and NO₃⁻ between 0.02 and 0.30 during AWD could increase rice yield by up to 4%. Yield improvements of 5 ∼ 7% were obtained when TOC and available potassium in background soil greater than 27.83 g kg⁻¹ and 0.18 g kg⁻¹, respectively, under water potential greater than −40 kPa (MWP). Nitrogen application in low rates and the addition of straw or biochar under MWP further amplified the beneficial effects of soil C and N, increasing yields by 2 ∼ 3%. Overall, biochemical edaphic factors were primarily responsible for driving rice yield responses to AWD. It can be suggested that combining management practices with AWD can reduce total water input requirement while concurrently increasing rice yield.