The emerging material class of complex-oxides, where manipulation of physical properties lead to new functionalities at their heterointerfaces, is expected to open new frontiers in Spintronics. For example, SrRuO3 is a promising material where external stimuli like strain, temperature and structural distortions control the stability of electronic and magnetic states, across its magnetic phase transition, useful for Spintronics. Despite this, not much has been studied to understand such correlations in SrRuO3. Here we explore the influence of electron-lattice correlation to electron-transport, at interfaces between SrRuO3 and Nb:SrTiO3 across its ferromagnetic transition, using a nanoscale transport probe and first-principles calculations. We find that the geometrical reconstructions at the interface and hence modifications in electronic structures dominate the transmission across its ferromagnetic transition, eventually flipping the charge-transport length-scale in SrRuO3. This approach can be easily extended to other devices where competing ground states can lead to different functional properties across their heterointerfaces.