When lepton-proton bound-state eigenvalue equations are derived from a local quantum field theory using second-order renormalization group procedure for effective particles (RGPEP) a la QCD for heavy quarkonia [1], the resulting non-perturbative corrections to the Schroedinger equation appear relevant to our understanding of the proton radius puzzle. The puzzle can be described as a conclusion that the proton radius in muon-proton bound states is smaller than in the electron-proton bound states by about 4% [2]. The RGPEP indicates instead that the radii ought to be discussed taking into account the scale difference between the effective theories required for handling different bound-states using the same Schroedinger equation [3]. Even more intriguing, the effective non-relativistic Schroedinger dynamics for lepton-proton atoms turns out to be operating in these very low-energy systems with the same type of momentum variables that also naturally appear in the light-front holography for quark-antiquark states [4,5] and in the interpretation of AdS/QFT duality in terms of the Ehrenfest theorem [6,7]. [1] E.g., see Harmonic oscillator force between heavy quarks, S. D. Glazek, Phys. Rev. D69, 065002 (2004). [2] Muonic hydrogen and the proton radius puzzle, R. Pohl et al., Ann. Rev. Nucl. Part. Sci. 63, 175 (2013). [3] Calculation of size for bound-state constituents, S. D. Glazek, Phys. Rev. D90, 045020, 26p (2014). [4] Hadronic spectrum of a holographic dual of QCD, G. F. de Teramond, S. J. Brodsky, Phys. Rev.Lett. 94, 201601 (2005). [5] Reinterpretation of gluon condensate in dynamics of hadronic constituents, S. D. Glazek, Acta Phys. Pol. B 42, 1933 (2011). [6] Model of the AdS/QFT duality, S. D. Glazek, A. P. Trawinski, Phys. Rev. D 88, 105025 (2013). [7] Effective confining potentials for QCD, A. P. Trawinski, S. D. Glazek, S. J. Brodsky, G. F. de Téramond, H. G. Dosch, Phys. Rev. D 90, 074017 (2014).