Protists, functionally divided into consumers, phototrophs, and parasites act as integral components and vital regulators of microbiomes in soil–plant continuums. However, the drivers of community structure, assembly mechanisms, co‐occurrence patterns, and the associations with human pathogens and different protistan trophic groups remain unknown. Here, we characterized the phyllosphere and soil protistan communities associated with three vegetables under different fertilization treatments (none and organic fertilization) at five growth stages. In this study, consumers were the most diverse soil protist group, had the role of inter‐kingdom connector, and were the primary biomarker for rhizosphere soils which were subjected to decreasing deterministic processes during plant growth. In contrast, phototrophs had the greatest niche breadth and formed soil protistan hubs, and were the primary biomarkers for both bulk soils and the phyllosphere. Parasites had minimal input to microbial co‐occurrence networks. Organic fertilization increased the relative abundance (RA) of pathogenic protists and the number of pathogen–consumer connections in rhizosphere soils but decreased protistan richness and the number of internal protistan links. This study advances our understanding of the ecological roles and potential links between human pathogens and protistan trophic groups associated with soil–plant continuums, which is fundamental to the regulation of soil–plant microbiomes and maintenance of environmental and human health. Protists are integral components of the microbiome in soil–plant systems, yet little is known about the dynamics of each protistan trophic group during plant growth and their association with human health. Here, we systematically characterized the protistan communities from the phyllosphere, rhizosphere, and bulk soils at different growth stages of three vegetables under different fertilization treatments (none and organic fertilization). Phototrophs were the dominant phyllosphere protists and also represented the major soil protistan module hub within co‐occurrence networks. Soil consumers were essential inter‐kingdom connectors being closely associated with potential human pathogens. Organic fertilization increased both pathogenic protists and pathogen–consumer connections in rhizosphere soils, suggesting that rhizosphere soil was a potential hotspot for pathogen transmission. Our findings present novel insights into the dynamics and ecological roles of each protistan trophic group and have implications for environmental applications of protists, fertilization management optimization, and supporting human health.