Given a conical affine special Kähler (CASK) manifold together with a compatible mutually local variation of BPS structures, one can construct a quaternionic-Kähler (QK) manifold. We call the resulting QK manifold an instanton corrected c-map space. Our main aim is to study the isometries of a subclass of instanton corrected c-map spaces associated to projective special real (PSR) manifolds with a compatible mutually local variation of BPS structures. We call the latter subclass instanton corrected q-map spaces. In the setting of Calabi-Yau compactifications of type IIB string theory, instanton corrected q-map spaces are related to the hypermultiplet moduli space metric with perturbative corrections, together with worldsheet, D(-1) and D1 instanton corrections. In the physics literature, it has been shown that the hypermultiplet metric with such corrections must have an SL(2,Z) acting by isometries, related to S-duality. We give a mathematical treatment of this result, specifying under which conditions instanton corrected q-map spaces carry an action by isometries by SL(2,Z) or some of its subgroups. We further study the universal isometries of instanton corrected q-map spaces, and compare them to the universal isometries of tree-level q-map spaces. Finally, we give an explicit example of a non-trivial instanton corrected q-map space with full SL(2,Z) acting by isometries and admitting a quotient of finite volume by a discrete group of isometries.