The influence of space on the structure (e.g. modularity) of complex ecological networks remains largely unknown. Here, we sampled an individual-based plant–pollinator network by following the movements and flower visits of marked bumblebee individuals within a population of thistle plants for which the identities and spatial locations of stems were mapped in a 50 50 m study plot. The plant–pollinator network was dominated by parasitic male bumblebees and had a significantly modular structure, with four identified modules being clearly separated in space. This indicated that individual flower visitors opted for the fine-scale division of resources, even within a local site. However, spatial mapping of network modules and movements of bumblebee individuals also showed an overlap in the dense center of the plant patch. Model selection based on Akaike information criterion with traits as predictor variables revealed that thistle stems with high numbers of flower heads and many close neighbours were particularly important for connecting individuals within the modules. In contrast, tall plants and those near the patch center were crucial for connecting the different modules to each other. This demonstrated that individual-based plant–pollinator networks are influenced by both the spatial structure of plant populations and individual-specific plant traits. Additionally, bumblebee individuals with long observation times were important for both the connectivity between and within modules. The latter suggests that bumblebee individuals will still show locally restricted movements within sub-patches of plant populations even if they are observed over a prolonged time period. Our individual-based and animal-centered approach of sampling ecological networks opens up new avenues for incorporating foraging behaviour and intra-specific trait variation into analyses of plant–animal interactions across space.