The Gouy phase is essential for accurately describing various wave phenomena, ranging from classical electromagnetic waves to matter waves and quantum optics. In this work, we employ phase-space methods based on the cross-Wigner transformation to analyze spatial and temporal interference in the evolution of matter waves characterized initially by a correlated Gaussian wave packet. First, we consider the cross-Wigner of the initial wave function with its free evolution, and second for the evolution through a double-slit arrangement. Different from the wave function which acquires a global Gouy phase, we find that the cross-Wigner acquires a Gouy phase difference due to different evolution times. The results suggest that temporal like-Gouy phase difference is important for an accurate description of temporal interference. Furthermore, we propose a technique based on the Wigner function to reconstruct the cross-Wigner from the spatial intensity interference term in a double-slit experiment with matter waves.