Reusing wastewater in agriculture is essential due to water scarcity but requires treatment technologies that preserve soil biological integrity. This study evaluated the impact of irrigation with wastewater treated by cold atmospheric plasma (CAP; 60 min exposure) on the soil microbiome during Festuca rubra L. and Sinapis alba L. cultivation. The experimental design included various CAP-wastewater dilutions evaluated in two replicates (n = 2), with microbial shifts assessed via 16S rRNA gene sequencing. CAP treatment reduced non-purgeable organic carbon (NPOC) while enriching the water with nitrogen, which significantly stimulated S. alba root growth. Metagenomic analysis confirmed high microbiome stability. Dominant phyla (Proteobacteria and Actinobacteriota) remained stable, and beta-diversity indices showed no statistically significant ecological shifts (R² = 0.420, p = 0.121). Furthermore, CAP-treated irrigation promoted beneficial taxa, specifically the genus Bacillus. These findings demonstrate that CAP wastewater treatment is a safe, environmentally responsible strategy for wastewater reclamation. It successfully supports nutrient cycling and agricultural production without compromising soil microbial homeostasis or health, offering a viable solution aligned with the principles of a circular economy.