We prove lower and upper semi-continuity of the Morse index for sequences of gradient Ricci shrinkers which bubble tree converge in the sense of past work by the author and Buzano. Our proofs rely on adapting recent arguments of Workman which were used to study certain sequences of CMC hypersurfaces and were in turn adapted from work of Da Lio-Gianocca-Rivi & egrave;re. Moreover, we are able to refine Workman's methods by using techniques related to polynomially weighted Sobolev spaces. This all also requires us to extend the analysis to handle when the shrinkers we study are non-compact, which we can do due to the availability of a suitable notion of finite weighted volume. Finally, we identify a technical condition which ensures the Morse index of an asymptotically conical shrinker is bounded below by the f-index of its asymptotic cone.