Summary: We study the non-perturbative properties of \(N = 2\) super conformal field theories in four dimensions using localization techniques. In particular we consider \(\mathrm{SU}(2)\) gauge theories, deformed by a generic \(\epsilon\)-background, with four fundamental flavors or with one adjoint hypermultiplet. In both cases we explicitly compute the first few instanton corrections to the partition function and the prepotential using Nekrasov’s approach. These results allow us to reconstruct exact expressions involving quasi-modular functions of the bare gauge coupling constant and to show that the prepotential terms satisfy a modular anomaly equation that takes the form of a recursion relation with an explicitly \(\epsilon\)-dependent term. We then investigate the implications of this recursion relation on the modular properties of the effective theory and find that with a suitable redefinition of the prepotential and of the effective coupling it is possible, at least up to the third order in the deformation parameters, to cast the S-duality relations in the same form as they appear in the Seiberg-Witten solution of the undeformed theory.