We show that plane Cremona groups over finite fields embed as dense subgroups into Neretin groups, that is, groups of almost automorphisms of rooted trees. We also show that if the finite base field has even characteristic and contains at least four elements, then the permutations induced by birational transformations on rational points of regular projective surfaces are even. In a second part, we construct explicit locally compact CAT(0) cube complexes, on which Neretin groups act properly. This allows us to recover in a unified way various results on Neretin groups such as that they are of type F-8. We also prove a new fixed-point theorem for CAT(0) cube complexes without infinite cubes and use it to deduce a regularization theorem for plane Cremona groups over finite fields.