In-situ coupled mechanical/electrical investigations on TPU-based composite materials filled with carbon black have been carried-out under continuous and cyclic mechanical loading, with simultaneous measurements of stress, strain and electrical conductivity in dependence on the strain rate and amplitude. The impact of mechanical deformation and thermal treatment on the structure/properties relationship has been investigated by employing SAXS/WAXS, DSC and TEM measurements. Higher conduction properties were obtained by a strain induced crystallization of TPU soft domains that impacted the local concentration of CB aggregates above the percolation threshold. The TPU hard domains were found to be more sensitive to thermal treatment: annealing at high temperature led to microcrystalline hard domains that strongly influenced the conductivity evolution upon mechanical deformation. Structural and morphological reorganizations induced by mechanical deformation and thermal treatment can be thus efficiently used to adjust the coupled electro-mechanical behavior of TPU-based composite materials.