We present a characterization, in terms of torsion-free generalized connections, for the integrability of various generalized structures (generalized almost complex structures, generalized almost hypercomplex structures, generalized almost Hermitian structures and generalized almost hyper-Hermitian structures) defined on Courant algebroids. We develop a new, self-contained, approach for the theory of Dirac generating operators on regular Courant algebroids with scalar product of neutral signature. As an application we provide a criterion for the integrability of generalized almost Hermitian structures (G, \mathcal J) and generalized almost hyper-Hermitian structures (G, \mathcal J_{1}, \mathcal J_{2}, \mathcal J_{3}) defined on a regular Courant algebroid E with scalar product of neutral signature, in terms of canonically defined differential operators on spinor bundles associated to E_{\pm} (the subbundles of E determined by the generalized metric G).