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Research on ecological communities, and plant–pollinator mutualistic networks in particular, has increasingly benefited from the theory and tools of complexity science. Nevertheless, up to now there have been few attempts to investigate the interplay between the structure of real pollination networks and their dynamics. This study is one of the first contributions to explore this issue. Biological invasions, of major concern for conservation, are also poorly understood from the perspective of complex ecological networks. In this paper we assess the role that established alien species play within a host community by analyzing the temporal changes in structural network properties driven by the removal of non-native plants. Three topological measures have been used to represent the most relevant structural properties for the stability of ecological networks: degree distribution, nestedness, and modularity. Therefore, we investigate for a detailed pollination network, 1) how its dynamics, represented as changes in species abundances, affect the evolution of its structure, 2) how topology relates to dynamics focusing on long-term species persistence; and 3) how both structure and dynamics are affected by the removal of alien plant species. Network dynamics were simulated by means of a stochastic metacommunity model. Our results showed that established alien plants are important for the persistence of the pollination network and for the maintenance of its structure. Removal of alien plants decreased the likelihood of species persistence. On the other hand, both the full network and the subset native network tended to lose their structure through time. Nevertheless, the structure of the full network was better preserved than the structure of the network without alien plants. Temporal topological shifts were evident in terms of degree distribution, nestedness, and modularity. However the effects of removing alien plants were more pronounced for degree distribution and modularity of the network. Therefore, elimination of alien plants affected the evolution of the architecture of the interaction web, which was closely related to the higher species loss found in the network where alien plants were removed.