We establish analogues for trees of results relating the density of a set $E \subset \mathbb{N}$, the density of its set of popular differences, and the structure of $E$. To obtain our results, we formalise a correspondence principle of Furstenberg and Weiss which relates combinatorial data on a tree to the dynamics of a Markov process. Our main tools are Kneser-type inverse theorems for sets of return times in measure-preserving systems. In the ergodic setting we use a recent result of the first author with Björklund and Shkredov and a stability-type extension (proved jointly with Shkredov); we also prove a new result for non-ergodic systems.