Climatic conditions can influence plant reproduction directly, but also via changes in plant traits, interactions with animals, and the surrounding environment. Such indirect effects can often be complex and involve multiple steps including climatic effects on interacting species, and on the context in which these interactions occur. The joint effects of climatic variation and indirect effects in terms of plant-animal interactions have sometimes been assessed at larger spatial scales. However, less is known about how microclimatic variation affects within-population variation in reproductive performance, in spite of that it is becoming increasingly clear that variation in climatic conditions can occur over very short distances. We studied the direct and indirect effects of microclimate on withinpopulation variation in reproductive performance of the plant Gentiana pneumonanthe in presence of the myrmecophagous and seed predator butterfly Phengaris alcon. We found that microclimatic effects on plant performance were mainly indirect, and that effects of temperature and moisture were interactive. The number of seeds per flower of G. pneumonanthe decreased in cold and moist microsites, and these effects were mediated by an increased oviposition by P. alcon in these microsites. The effects of soil temperature and moisture on the incidence of oviposition and plant performance were mediated by effects on plant phenology, density and phenology of neighbouring host plants, and host ant abundance. Plants that flowered earlier and where host ants were more abundant, and especially plants surrounded by fewer and later-flowering neighbours, produced fewer seeds per flower because of a higher incidence of oviposition. Our results demonstrate that effects of microclimatic variation on plant reproductive performance can be mostly indirect and largely mediated by species interactions. These findings highlight that among individual variation in small-scale environmental conditions within populations can cause variation in individual plant performance through multiple pathways.