The search for high Li-ion conducting ceramics has regained tremendous interest triggered by the renaissance of the all-solid-state battery. Within this context we herein reveal the impact of structural polymorphism of lithium copper pyroborate Li6CuB4O10 on its ionic conductivity. Using combined in situ synchrotron X-ray and neutron powder diffraction, a structural and synthetic relationship between alpha- and beta-Li6CuB4O10 could be established and its impact on ionic conductivity evolution was followed using electrochemical impedance spectroscopy. We show that the high temperature form of Li6CuB4O10 exhibits a high Li-ion conductivity (2.7 mS cm(-1) at 350 degrees C) and solve its crystal structure for the first time. Our results emphasize the significant impact of structural phase transitions on ionic conductivity and show possible high Li-ion mobility within borate based compounds.