Interlocus sexual conflict (ISC) arises due to antagonistic interactions between the sexes. Recent evidence suggests that the intensity of ISC could reduce due to habitat complexity and spatial structure, especially if it results in reduced encounter rate between sexes. Hence, spatial structuring, a common attribute of most natural populations, can potentially bring down the intensity of ISC. We tested this theory using laboratory populations of Drosophila melanogaster. We set up cohorts in three-patch habitat systems as either interconnected (structured) or unconnected (unstructured). Following a fully crossed design, we measured ISC by comparing reproductive output and starvation resistance of singly mated females and those continuously housed with surplus males. We show that continued exposure to males leads to significant fitness costs, indicating ISC. The experimental habitat type did not affect ISC. However, we found significant reproductive and survival costs arising from structured population. Our results are also robust to the alteration in female condition. Therefore, it appears that spatial structure per se cannot decrease ISC, but impose additional survival costs. We further showed such survival cost to be sex-specific, possibly reflecting female-biased spontaneous dispersal.