Brønsted acidic zeolites are ubiquitous catalysts in fuel and chemical production. Broadening the catalytic diversity of a given zeolite requires strategies to manipulate the acid site placement at framework positions within distinct microporous locations. Here, we combine experiment and theory to elucidate how intermolecular interactions between organic structure-directing agents (OSDAs) and framework Al centers influence the placement of H+ sites in distinct void environments of MFI zeolites and demonstrate the catalytic consequences of active site location on kinetically controlled (403 K) toluene methylation to xylene regioisomers. Kinetic measurements, interpreted using mechanism-derived rate expressions and transition state theory, alongside density functional theory (DFT) calculations show that larger intersection environments similarly stabilize all three xylene isomer transition states without altering well-established aromatic substitution patterns (ortho/para/meta ∼ 60%:30%:10%), while smaller channel environments preferentially destabilize transition states that form bulkier ortho- and meta-isomers, thereby resulting in high intrinsic para-xylene selectivity (∼80%). DFT calculations reveal that the flexibility of nonconventional OSDAs (e.g., 1,4-diazabicyclo[2.2.2]octane) to reorient within MFI intersections and their ability to hydrogen-bond to form protonated complexes favor the placement of Al in smaller channel environments compared to conventional quaternary OSDAs (e.g., tetra-n-propylammonium). These molecular-level insights establish a mechanistic link between OSDA structure, active site placement, and transition state stability in MFI zeolites and provide active site design strategies that are orthogonal to crystallite design approaches harnessing complex reaction-diffusion phenomena to enhance regioisomer selectivity in the industrial production of valuable polymer precursors.