Nanoimprinting the photoactive layer of bulk heterojunction (BHJ) organic solar cells is a promising technique for enhancing device performance via improved light absorption. Here, we demonstrate that imprinting poly(3-hexylthiophene) (P3HT) and fullerene BHJ blends leads to adverse morphological changes within the photoactive nanopattern which have been previously overlooked. In particular, nanoimprinting induces a factor of 2 difference in polymer:fullerene composition between the nanopattern posts and interconnecting flash layer that inadvertently moves the composition outside the range for optimal performance. This occurs because of the strong tendency of regioregular P3HT to crystallize since imprinting blends based on amorphous regiorandom P3HT have uniform nanopattern composition. Based on these results, we outline promising design strategies, such as nanoimprinting amorphous polymers, to serve as guidelines for fabricating high-performance nanopatterned BHJ solar cells capable of maximized light absorption.