In this work, we analyze the semi-leptonic decays $bar B^0/D^0 to (a_0(980)^{pm}topi^{pm}eta) l^{mp} u$ within light-cone sum rules. The two and three-body light-cone distribution amplitudes (LCDAs) of the $B$ meson and the only available two-body LCDA of the $D$ meson are used. To include the finite-width effect of the $a_0(980)$, we use a scalar form factor to describe the final-state interaction between the $pieta$ mesons, which was previously calculated within unitarized Chiral Perturbation Theory. The result for the decay branching fraction of the $D^0$ decay is in good agreement with that measured by the BESIII Collaboration, while the branching fraction of the $bar B^0$ decay can be tested in future experiments.