The combined effect of changes in pollinator communities, and the direct impact of soil and climate variation on plant-pollinator interactions can strongly affect the reproductive success of flowering plants. However, knowledge of the adaptative potential of plants to complex ecological networks and the underlying genetic mechanisms is still limited. Based on a pool-sequencing approach of 21 natural populations of Brassica incana in Southern Italy, we combined a genome-environmental association (GEA) analysis with a genome scan for signature of selection to discover genetic variants associated with pollinator communities, edaphic and climatic variation. We demonstrated that B. incana is locally adapted to both single pollinator species and the overall pollinator interactions. Interestingly, we observed a significant number of genetic variants shared between the soil texture (fine silt) and the visits of bumblebees and hoverflies, while few genetic variants involved in both pollinator and climate variation were identified. Our results highlight the adaptive potential of generalist species to complex biotic interactions, and the importance of considering multiple environmental factors to describe their adaptive landscape.