Deconfinement in gauge theories and symmetry-protected topological order are central to our understanding of strongly correlated quantum materials. A question of crucial importance regards the robustness of these concepts to the inclusion of fermionic matter fields. In light of this question, we study here a simple toy model, three antiferromagnetically coupled Kondo impurities, and demonstrate the existence of two distinct quantum phases which both preserve all symmetries of the model and thereby transcend the Landau-Ginzburg paradigm. An interpretation of the phase with dominant magnetic frustration in terms of symmetry protected topological order is corroborated by an irrational ground state degeneracy (suggestive of decoupled anyons) and a Wilson loop-like order parameter. We furthermore characterize the quantum transition between the two phases, which is driven by the proliferation of instantons in the emergent gauge field. Our work paves the way towards a better understanding of deconfinement in gauge theories interacting with matter fields.