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Traditionally, ecologists have focused on direct effects of habitat area and arrangement on individual species or pairwise species interactions. Indirect effects of habitat heterogeneity on multiple interacting species are often neglected or lack experimental support. In a factorial field experiment, we explored the direct and indirect effects of habitat area, fragmentation, and matrix composition on a community of flower-visiting insects in red clover. Habitat area, fragmentation, and density of inflorescences of red clover all influenced the insect pollinators and, in turn, the production of clover seeds. The strongest direct effect was on pollinator visitation, which was substantially higher in small clover patches surrounded by bare-ground than in larger patches embedded within grass. Structural equation modeling indicated that the observed matrix-dependent changes in pollinator visitation propagated across a tri-trophic system: higher visitation rates positively correlated with a higher seed set, which in turn was positively correlated with abundances of seed predators and their parasitoids. Therefore, this study suggests that habitat area and matrix composition can strongly influence the structure of species interaction webs through indirect effects, and also emphasizes that these effects can be propagated through mutualistic as well as trophic interactions.