We consider the non-perturbative superpotential for a class of four-dimensional $mathcal N=1$ vacua obtained from M-theory on seven-manifolds with holonomy $G_2$. The class of $G_2$-holonomy manifolds we consider are so-called twisted connected sum (TCS) constructions, which have the topology of a K3-fibration over $S^3$. We show that the non-perturbative superpotential of M-theory on a class of TCS geometries receives infinitely many inequivalent M2-instanton contributions from infinitely many three-spheres, which we conjecture are supersymmetric (and thus associative) cycles. The rationale for our construction is provided by the duality chain of arXiv:1708.07215, which relates M-theory on TCS $G_2$-manifolds to $E_8times E_8$ heterotic backgrounds on the Schoen Calabi-Yau threefold, as well as to F-theory on a K3-fibered Calabi-Yau fourfold. The latter are known to have an infinite number of instanton corrections to the superpotential and it is these contributions that we trace through the duality chain back to the $G_2$-compactification.