Climate change can alter species phenologies and therefore disrupt species interactions. Habitat destruction can damage biodiversity and population viability. However, we still know very little about the potential effects of these two factors on the diversity and structure of interaction networks when both act simultaneously. Here we developed a mutualistic metacommunity model to explore the effects of habitat destruction and phenological changes on the diversity and structure of plant–pollinator networks. Using an empirical data set of plant and pollinator interactions and their duration in days, we simulated increasing levels of habitat destruction, under projected scenarios of phenological shifts as well for historically recorded changes in phenologies. On one hand, we found that habitat destruction causes catastrophic collapse in global diversity, as well as inducing alternative states. On the other hand, phenological shifts tend to make interactions weaker, increasing local extinction rates. Together, habitat destruction and phenological changes act synergistically, making metacommunities even more vulnerable to global collapse. Metacommunities are also more vulnerable to collapses under scenarios of historical change, in which phenologies are shortened, not just shifted. Furthermore, connectance and nestedness tends to decrease gradually with habitat destruction before the global collapse. Small phenological shifts can raise connectance slightly, due novel interactions appearing in a few generalist species, but larger shifts always reduce connectance. We conclude that the robustness of mutualistic metacommunities against habitat destruction can be greatly impaired by the weakening of positive interactions that results from the loss of phenological overlap.