Extreme drought events occur more frequently due to climate change. Soil water loss through evaporation is therefore significantly intensified. This study introduces an environment‐friendly and sustainable bio‐mediated technique, known as microbially induced calcite precipitation (MICP), for water evaporation suppression in clayey soils. Through lab‐scale evaporation tests, we investigate the effects of cementation solution concentration (0.5, 1.0, and 1.5 mol/L) and MICP treatment procedure (one‐phase and two‐phase MICP methods) on both macroscale (e.g., water loss, desiccation cracking) and microscale (e.g., microstructure variations) behaviors of soils. Experimental results show that MICP is capable of improving water retention capacity and enhancing the inter‐particle bonding of clayey soils. Both water evaporation rate and total water loss decrease with the increasing concentration of cementation solution and the number of MICP treatment cycle. For most testing samples, both one‐phase and two‐phase MICP treatment methods have a similar influence on soil properties. Further microstructure characterizations reveal four key factors contributing to the improved soil response under drying, including dense surface crust, remediated desiccation cracks, smaller pore size and residual solutes. Dense structure of surface crust suppresses the migration of water vapor into the atmosphere. Calcite crystals tend to reduce the evaporation surface if precipitated within cracks, and clog the movement of pore water if precipitated within the soil pore space. This study is expected to improve the fundamental understanding of soil‐atmosphere interactions under MICP treatment and provide insights into the potential application of bio‐mediated technologies as a nature‐based solution for drought mitigation in arid and semi‐arid region.