Conjugated polymers are an important class of materials for organic electronics applications. There, the relative alignment of the electronic energy levels at ubiquitous organic/(in)organic interfaces is known to crucially impact device performance. On the prototypical example of poly(3-hexylthiophene) and a fluorinated derivative, the energies of the ionization and affinity levels of pi-conjugated polymers are revealed to critically depend on the orientation of the polymer backbones with respect to such interfaces. Based on extensive first-principles calculations, an intuitive electrostatic model is developed that quantitatively traces these observations back to intrinsic intramolecular surface dipoles arising from the pi-electron system and intramolecular polar bonds. The results shed new light on the working principles of organic electronic devices and suggest novel strategies for materials design.