Weyl fermions in an external magnetic field exhibit the chiral anomaly, a non-conservation of chiral fermions. In a Weyl semimetal, a spatially inhomogeneous Weyl node separation causes similar effect by creating an intrinsic pseudo-magnetic field with an opposite sign for nodes of opposite chirality. In the present work we study the interplay of external and intrinsic fields. In particular, we focus on quantum oscillations due to bulk-boundary trajectories. When caused by an external field, such oscillations are a proven experimental technique to detect Weyl semimetals. We show that the intrinsic field leaves hallmarks on such oscillations by decreasing the period of the oscillations in an analytically traceable manner. The oscillations can thus be used to test the effect of an intrinsic field and to extract its strength.