A number of experiments have demonstrated that destructive quantum interference (QI) effects in molecular junctions lead to very low conductances even at room temperature. On the other hand, another recent experiment showed increasing conductance with temperature which was attributed to decoherence effects destroying QI at finite temperatures. Here we study the influence of finite temperatures and electron-phonon interactions on QI in molecular junctions. Two different models leading to two inherently different types of QI effects are considered. Each model is exemplified by specific molecules and studied using first-principles calculations. We find that the molecules exhibiting QI show a much stronger temperature dependence of the conductance compared to molecules without QI. However, the large QI-induced suppression of the conductance remains, showing that QI effects are indeed robust against finite temperatures and inelastic scattering.