We predict the twist-2 Transverse Momentum Dependent parton distribution functions (TMDs) of the pion, namely the unpolarized quark TMD, f 1 (x, k ⊥ ), and the transversely polarized quark TMD, also known as the Boer-Mulders function, h ⊥ 1 (x, k ⊥ ), using a holographic light-front pion wavefunction with dynamical spin effects. These spin effects, in conjunction with gluon rescattering, are crucial to predict a non-zero holographic Boer-Mulders function. We investigate the use of a non-perturbative SU(3) gluon rescattering kernel, thus going beyond the usual approximation of perturbative U(1) gluons. We also predict the generalized Boer-Mulders shifts in order to compare with the available lattice data.