In recent years, global beach erosion has intensified, presenting severe challenges for the sustainable management and conservation of coastal environments. To address this issue, we conducted a 16-month investigation at Niginohama Beach in western Fukuoka, integrating RTK-GNSS surveys, grain-size analyses, vegetation coverage assessments, and in situ wind measurements. Within the study area, we identified Vegetation-induced Micro Topographic Features (VMTFs)—micro-dunes formed and stabilized through interactions between wind forces and plant root systems. The results demonstrated that vegetation coverage fluctuated seasonally and showed a strong positive correlation with changes in beach volume. VMTFs substantially modified airflow, reduced near-surface wind velocities, and promoted localized sediment deposit. Grain-size analyses further indicated well-sorted, fine-grained distributions regulated by vegetation and microtopography. These findings highlight the central role of VMTFs in stabilizing sandy coasts and demonstrate their broader relevance to wind-dominated coastal systems worldwide. Looking forward, the incorporation of VMTFs into “green infrastructure” approaches provides a promising, ecologically grounded strategy to mitigate erosion and support sustainable coastal management.