Flavin-tryptophan dyads linked by oligoproline chains were used to probe how proline cis-trans isomerization modulates spindynamics under photo-CIDNP conditions. Field-cycling NMR revealed that minor cis-containing conformers form compact geometries that support intramolecular biradical recombination. These states display the features of J-resonance photo-CIDNP: uniform emissive polarization and pronounced maxima at 5-20 mT, while their signals vanish at high fields. In contrast, the dominant all-trans (PPII) conformers and longer linkers produce only Δg-dominated patterns consistent with intermolecular radical encounters. Time-resolved photo-CIDNP confirmed that intermolecular processes prevail in most systems, with the fourproline dyad showing additional intramolecular contributions. The results establish that proline isomerization serves as a structural switch that governs the donor-acceptor distance and consequently, the balance between intra- and intermolecular spin-selective pathways. The study further highlights field-cycling photo-CIDNP as a promising tool for identifying transient biradical states in biomolecular model systems.