Pockels-based Mueller polarimetry is presented as a novel diagnostic technique for studying time and space-resolved and in-situ the interaction between an organic sample (a layer of onion cells) and non-thermal atmospheric pressure plasma. The effect of plasma is complex, as it delivers electric field, radicals, (UV) radiation, non-uniform in time nor in space. This work shows for the first time that the plasma-surface interaction can be characterized through the induced electric field in an electro-optic crystal (birefringence caused by the Pockels effect) while at the same moment the surface evolution of the targeted sample is monitored (depolarization) which is attached to the crystal. As Mueller polarimetry allows for separate detection of depolarization and birefringence, it is possible to decouple the entangled effects of the plasma. In the sample three spatial regions are identified where the surface evolution of the sample differs. This directly relates to the spatial in-homogeneity of the plasma at the surface characterized through the detected electric field. The method can be applied in the future to investigate plasma-surface interactions for various targets ranging from bio-films, to catalytic surfaces and plastics/polymers.