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In this PhD thesis we deal with several theoretical and phenomenological apsects of metric-affine theories of gravity. Concretely, we first give a broad introduction to the necessary tools to understand the framework and elaborate on some subtleties of the minimal coupling prescription between geometry and matter in presence of torsion and nonmetricity. Then we dedicate the central part of the thesis to study the structure of Ricci Based gravity (RBG) theories, which will be of later use to understand generic properties of metric-affine theories. We begin by analysing the structure of the RBG field equations and nontrivial aspects of their solution space. We then analyse the abrosption spectra of some spherically symmetric solutions. Then, we show that, if the projective symmetry in these theories is explicitly broken, then there arise ghost degrees of freedom, and we argue that this will be a generic feature of metric-affine gravity theories. Having done this, we analyse metricafine theories through the EFT lens, showing how the nonmetricity tkes a particular form in generic theories where the symmetrised Ricci tensor appears in the action beyond the Einstein-Hilbert term. This sources effective interactions that we use to place tight constraints to these theories. In the third part of the thesis we present a miscelanea of works which are not so related to the structure of RBG theories. We begin by studying a model for spontaneous breaking of Lorentz symmetry, namely the bumblebee model, in the metric-affine approach. In the following chapter we generalise a conformal invariant definition of proper time given by Perlick to the case with general nonmetricity. Finally, we present arguments that show that the recently proposed D4EGB theory is not well defined in its original form. We finish with a brief outlook.