The weak noncovalent interactions and flexibility of ligands play a key role in enantioselective metal-catalyzed reactions. In transition metal complexes and their catalytic applications, the experimental assessment and the design of key interactions is as difficult as the prediction of the enantioselectivities, especially for flexible, privileged ligands such as chiral phosphoramidites. Therefore, the interligand interactions in cis-(PdL2Cl2)-L-II phosphoramidite complexes were investigated by NMR spectroscopy and computations. We were able to induce a strong conformational preference by breaking the symmetry of the C-2-symmetric side chain of one of the ligands, and shift the equilibrium between hetero- and homocomplexes towards heterocomplexes because of interligand interactions in the cis-complexes. The modulation of aryl substituents was exploited, along with the solvent effect. The combined CH-pi and pi-pi interactions reveal design patterns for binding and folding of chiral ligands and catalysts.