Unveiling the microscopic origins of quantum phases dominated by the interplay of spin and motional degrees of freedom constitutes one of the central challenges in strongly correlated many-body physics. When holes move through an antiferromagnetic spin background, they displace the positions of spins, which induces effective frustration in the magnetic environment. However, a concrete characterization of this effect in a quantum many-body system is still an unsolved problem. Here we present a Hamiltonian reconstruction scheme that allows for a precise quantification of hole-motion-induced frustration. We access non-local correlation functions through projective measurements of the many-body state, from which effective spin-Hamiltonians can be recovered after detaching the magnetic background from dominant charge fluctuations. The scheme is applied to systems of mixed dimensionality, where holes are restricted to move in one dimension, but SU(2) superexchange is two-dimensional. We demonstrate that hole motion drives the spin background into a highly frustrated regime, which can quantitatively be described by an effective J1–J2-type spin model. We exemplify the applicability of the reconstruction scheme to ultracold atom experiments by recovering effective spin-Hamiltonians of experimentally obtained 1D Fermi-Hubbard snapshots. Our method can be generalized to fully 2D systems, enabling promising microscopic perspectives on the doped Hubbard model.