Abstract: We generalize the Chern-Simons modified gravity to the metric-affine case and impose projective invariance by supplementing the Pontryagin density with homothetic curvature terms which do not spoil topologicity. The latter is then broken by promoting the coupling of the Chern-Simons term to a (pseudo)-scalar field. The solutions for torsion and nonmetricity are derived perturbatively, showing that they can be iteratively obtained from the background fields. This allows us to describe the dynamics for the metric and the scalar field perturbations in a self-consistent way, and we apply the formalism to the study of quasi normal modes in a Schwarzschild black hole background. Unlike in the metric formulation of this theory, we show that the scalar field is endowed with dynamics even in the absence of its kinetic term in the action. Finally, using numerical methods we compute the quasinormal frequencies and characterize the late-time power law tails for scalar and metric perturbations, comparing the results with the outcomes of the purely metric approach.