Seed-associated microbiomes represent a critical yet underutilised frontier in synthetic community (SynCom) design, particularly in forage legumes such as lucerne (Medicago sativa L.), where early microbial assembly can shape plant development. We developed ecologically-informed SynComs using seed-derived bacterial isolates from Medicago crop wild relatives (CWRs), prioritising genera that co-occur with the cultivated lucerne seed microbiota. Two three-strain SynComs and one six-strain ‘Mix’ SynCom were applied via seed inoculation. Plants were glasshouse-grown; a subset was transferred to a separate phenomics facility, exposed to contrasting water regimes, and later returned to the glasshouse for post-stress recovery. A multi-tiered approach combining phenotyping, high-throughput imaging, and 16S rRNA profiling captured plant–microbiome dynamics. SynCom inoculation consistently enhanced germination and early growth, with the ‘Mix’ SynCom producing the strongest early-stage phenotypic gains. Microbiome profiling revealed treatment-specific restructuring, showing selective enrichment and microbial coalescence. While SynCom effects were most pronounced early, their influence under drought and later stages was variable and context dependent. This study positions seed-based, CWR-derived SynComs as effective modulators of early plant–microbiome interactions. By integrating ecological selection with temporal phenotyping, we present a scalable framework for microbiome-informed crop improvement and a translational path toward seed-based microbial solutions in sustainable agriculture.