The degradation of the Cu6Sn5 intermetallic compound layer caused by pore formation in fine pitch Cu/Sn microbump interconnects is reported in this study. Die-to-die stacking was carried out using the solid–liquid interdiffusion principle. The diameters of the microbumps on the top (Cu/Sn) and bottom die (Cu) were 15 and 25μm, respectively. The stacking process was carried out in air atmosphere at 240 and 260°C with varying holding time at the peak temperature 10s, 1, 2, 3, 4, 10 and 20min. Flux and flux-containing no-flow underfill were used for stacking. Subsequent thermal storage experiments were done in N2 and in air at 240 and 260°C for 10min, 20min, 1, 3, 24 and 96h. The pores start to form after 1min bonding at the edges of Cu6Sn5 exposed to flux/underfill. These pores propagate to the center of the interconnect with longer bonding time till the complete Cu6Sn5 layer is affected (after 4min). The possible mechanism of the pore formation is the dissolution of Sn atoms from the Cu6Sn5 matrix due to the reaction between Cu6Sn5 and flux residues. The remaining pore layer has the composition of Cu3Sn. The results of a subsequent thermal storage show, that a complete transformation of Cu6Sn5 into Cu3Sn without further degradation is possible after the removal of the flux residues.