Understanding the vortex interactions and wake transitions for flapping flexible foils is important because of their increased usage in bioinspired aquatic and aerial robotic propulsors. Although wake transitions have been studied for rigid foils, we experimentally investigate how flexibility alters the transitions and vortex interactions for flexible foils, which are closer to the natural flapping foils in fish, birds and insects. We conduct the experiments in a flowing soap film on a pitching airfoil with a flexible filament at its trailing edge (TE). We find that, apart from the Strouhal number (${\textit{St}}$), flexural rigidity (${\textit{EI}}$) is important to determine the transitions. We vary ${\textit{EI}}$ of the flexible filament by three orders of magnitude and also investigate an extreme case of ${\textit{EI}} \rightarrow \infty$. Flexibility triggers the shedding of multiple small ‘secondary vortices’ (SVs) along with big ‘primary vortices’ (PVs), unlike only PVs for the rigid foil. Continuous deformations of the flexible filament play crucial roles in determining the interaction of boundary layer vortices and trailing edge vortices and, ultimately, the generation and evolution of PVs and SVs. We identify five vortex interaction mechanisms (VIMs). Depending on how SVs interact with PVs, the wake assumes different patterns. We construct the ${\textit{St}}$–${\textit{EI}}$ phase maps for wake transitions and newly identified VIMs. We devise a non-dimensional parameter $\varUpsilon$, referred to as ‘Yashavant number’. One order increase in $\varUpsilon$ reduces the number of VIMs by one. Instead of following the usual transition route, the flexible foil reveals counterintuitive transition trends that strongly depend on the filament ${\textit{EI}}$.