Microorganisms form dynamic communities with plants, providing benefits such as nutrient acquisition and stress resilience. Understanding how these microorganisms are affected by environmental factors such as growth conditions and soil characteristics are essential for harnessing these communities for sustainable agriculture practices and their response to climate change. The microbiome associated to Lupinus angustifolius, a legume native in Europe, with a high protein value and stress resilience was characterized for the first time. Using 16S rRNA gene and ITS amplicon sequencing, we characterized the compositional and temporal changes of the bacterial and fungal communities associated to the soil, rhizosphere, and plant compartments where Lupinus angustifolius grows naturally. Our results suggest that the main difference in the soil microbial communities is related to the edaphic properties, although environmental factors such as temperature, humidity or rainfall also influenced the composition of the soil microbial communities. We also characterized the bacterial communities associated with the rhizosphere, roots, nodules, and leaves of wild plants collected in the field and compared them against plants obtained under greenhouse conditions. In the plant compartments, the bacterial composition appeared to be more affected by the growing conditions (field vs greenhouse), than by soil characteristics or location. These results can be used to identify key taxa that may play crucial roles in the development and adaptation of the host plant and its associated microbiota to environmental changes and highlight the importance of characterizing the plant microbiomes in their natural habitats. Soil, influenced by climatic seasons, shapes the plant microbiome assembly. Lupinus recruits a core microbiome across rhizosphere, roots, nodules, and leaves, that is stable across locations. However, cultivation conditions may alter microbiome dynamics, impacting the adaptability of its components. Wild plants show a resilient and adaptable microbiome while germination and cultivation in greenhouse conditions alter its composition and vulnerability.