In addition to the glass transition, vitrimers undergo a topological transition from viscoelastic liquid to viscoelastic solid behavior when the network rearrangements facilitated by dynamic bond exchange reactions freeze. The microscopic observation of this transition is elusive. Model polyisoprene vitrimers based on imine dynamic covalent bonds were synthesized by reaction of α,ω-dialdehyde-functionalized polyisoprenes and a tris(2-aminoethyl)amine. In these dynamic networks nanophase separation of polymer and reactive groups leads to the emergence of a relevant length scale characteristic for the network structure. We exploited the scattering sensitivity to structural features at different length scales to determine how dynamical and topological arrests affect correlations at segmental and network levels. Chains expand obeying the same expansion coefficient throughout the entire viscoelastic region, i.e., both in the elastomeric regime and in the liquid regime. The onset of liquid-like behavior is only apparent at the mesoscale, where the scattering reveals the reorganization of the network triggered by bond exchange events. The such determined "microscopic" topological transition temperature is compared with the outcome of "conventional" methods, namely viscosimetry and differential scanning calorimetry. We show that using proper thermal (aging-like) protocols, this transition is also nicely revealed by the latter.