We study the addition of flavor to the gravity dual of N=4 three-dimensional gauge theories obtained by wrapping Nc D4-branes on a two-cycle of a non-compact Calabi-Yau two-fold. In this setup the flavor is introduced by adding another set of D4-branes that are extended along the non-compact directions of the Calabi-Yau which are normal to the cycle which the color branes wrap. The analysis is performed both in the quenched and unquenched approximations. In this latter case we compute the backreacted metric and we show that it reproduces the running of the gauge coupling. The meson spectrum and the behavior of Wilson loops are also discussed and the holographic realization of the Higgs branch is analyzed. Other aspects of this system studied are the entanglement entropy and the non-relativistic version of our backgrounds.