We study the dynamics of perturbations representing deviations from perfect isotropy in the context of the emergent cosmology obtained from the group field theory formalism for quantum gravity. Working in the mean field approximation of the group field theory formulation of the Lorentzian EPRL model, we derive the equations of motion for such perturbations to first order. We then study these equations around a specific simple isotropic background, characterised by the fundamental representation of ##IMG## [http://ej.iop.org/images/0264-9381/35/1/015014/cqgaa986aieqn001.gif] $rm SU(2)$ , and in the regime of the effective cosmological dynamics corresponding to the bouncing region replacing the classical singularity, well approximated by the free GFT dynamics. In this particular example, we identify a region in the parameter space of the model such that perturbations can be large at the bounce but become negligible away from it, i.e. when the background enters the non-linear regime. We also study the departures from perfect isotropy by introducing specific quantities, such as the surface-area-to-volume ratio and the effective volume per quantum , which make them quantitative.