The aim of this work is to study the holographic dual to the gauge theory with a nonzero gluon condensate. We check for consistency the holographic way of describing the condensate and calculate the expectation value of a small Wilson loop in the presence of the gluon condensate, thus obtaining the relevant coefficient in the operator product expansion of the small loop in different holographic models. We also study the effect of the condensate on the Gross-Ooguri phase transition in the correlator of two circular Wilson loops in parallel and concentric configurations. In the numerical study of the concentric case, we find that the phase transition changes its order when the size of the loops is of order of the gluon condensate. We report this change of the phase transition order to be a new effect in Wilson loop correlators.