Engineering the properties of conjugated materials in the solid state is an unsolved, ongoing challenge important to fundamental understanding of how non‐covalent interactions dictate packing and key properties, as well as the development of technologies based in organic optoelectronics. The most common design paradigm of such materials divide them into a “main chain” with extended conjugation, the chemical structure of which determines optoelectronic properties, and “side chains” not conjugated to the backbone, which provide solubility when they are long alkyl chains. This paper describes comparisons between phenylene‐ethynylene molecules in which slight changes to the structure of “side chains”—swapping hydrogen and fluorine atomic position on an aromatic ring—results in unexpectedly large changes in the solid‐state optical properties. In a pair of anisyl‐terminated three‐ring phenylene‐ethynylenes, switching the side chain arenes of benzyl esters from 2,4,6‐trifluoro to 2,3,6‐trifluoro results in a shift in fluorescence emission spectra of over 100 nm, as well as the opposite direction of force‐induced shifting of emission. Through a combination X‐ray crystal structures, electronic structure calculations, and comparisons with other derivatives, we describe how the 2,4,6‐trifluorinated side chains yield cofacial fluoroarene‐arene stacking interactions that twist the PE backbone out of conjugation, while the 2,3,6‐trifluoro side chains do not stack, instead yielding more coplanar PE backbones that form intermolecular aggregates. Overall, this work demonstrates how slight modifications to parts of conjugated materials normally considered ancillary to optoelectronic properties can determine their solid‐state properties, epitomizing the challenge of rational design but at the same time offering opportunities for materials discovery and improved understanding of non‐covalent interactions.