Abstract Strawberry drinks are considered as functional food products due to their high content of health-promoting compounds such as polyphenols. High-pressure homogenization (HPH) results in microbial inactivation while significantly disrupting the plant matrix. This study evaluated the effect of HPH (up to 200 MPa) and number of cycles (at 200 MPa) on the physicochemical, structural and functional attributes of strawberry nectar, with and without the common filtration step that removes part of the polyphenols. HPH reduced particle size, and negatively affected the stability against sedimentation. Surprisingly, viscosity of the filtered drink at low shear-rates increased after homogenization. Color and anthocyanin content were only slightly affected by pressure levels, while total polyphenol concentration was not affected by pressure levels yet significantly increased (up to 30%) following cycling, possibly because of polyphenol extraction from the pulp and achenes. Thus, HPH cycling can be a promising technology for enhancing health-promoting capacity of polyphenol-rich matrices. Industrial relevance Enhancing the health promoting potential of foods is a major driving force for the utilization and further development of novel process technologies. High pressure homogenization is known to decrease the microbial count while significantly disrupting the plant matrix due to the extensive shear forces. This disruption may have, on one hand, major impact on the techno-functional properties like physical stability, rheology and color, yet on the other hand it might result in the release of various bioactive compounds from the plant matrix. Strawberry nectar is a valuable commodity that is often considered as a functional product due to the range of health promoting components, including polyphenolic compounds such as anthocyanins and phenolic acids. Yet very little information exists in the literature regarding the outcome of high pressure homogenization parameters on the properties of strawberry nectars/juices. The data provided in the presented manuscript can fill such a gap regarding strawberry based drinks and also provide a reference for the effect of such technologies on other plant based products.