Plant microbiota assembly is a dynamic process shaped by a succession of microbial dispersal events, interactions, and environmental fluctuations. While most research emphasizes the roles of resident and core taxa in driving microbiome structure and plant health, the ecological significance of transient microbial members (taxa temporarily present in plant tissue and then disappearing from microbiota) remains underexplored. In this opinion article, we propose that these ephemeral microorganisms may act as ‘transient microbial architects’, capable of generating legacy effects that influence the trajectory of microbiota assembly and long-term plant fitness. By reviewing the available temporal studies, we show that transient taxa often collectively represent the most diverse and abundant plant microbiota members compared to core taxa. We highlight how priority effects, niche modification, and microbe–microbe interactions mediated by transient taxa, can alter community composition, modulate the recruitment of symbionts, and shape plant responses to biotic and abiotic stressors. We identify outstanding questions and propose methodological advances to address them, including high-resolution longitudinal sampling and integrative omics approaches, that will enable the detection and functional characterization of these elusive taxa. Finally, we discuss the potential for harnessing transient microbial architects in microbiome engineering strategies for sustainable agriculture, emphasizing the need for targeted interventions during critical plant developmental windows. By recognizing and harnessing the legacy effects of these transient members, we gain access to previously overlooked ecological levers for shaping plant–microbe interactions.