Bioactive compounds, such as polyphenols and anthocyanins, are rapidly affected by exogenic factors such as oxygen, light, as well as pH and temperature. The challenge to preserve polyphenols and anthocyanins suggests the application of high hydrostatic pressure for the sanitation of products rich in bioactive compounds, such as red-fruits derivatives.The aim of this paper is to study the effects of high pressure (HP) on the polyphenol and anthocyanin content of several red fruit-based products (strawberry and wild strawberry mousses, pomegranate juice). The processing conditions were set at 500 MPa, 50°C, 10 min for the mousse samples and 400 MPa, 25 °C and 5 min for the pomegranate juice samples, according to the results of the process cycle optimization obtained in a previous experimental campaign. The products, microbiologically stable, were stored under refrigerated conditions for 3 months, with the bioactive molecules being determined weekly.The results demonstrate the dependence of the anthocyanin and polyphenol content on the processing conditions, raw materials and storage conditions. The observed stability of these molecules could be transient, due to the residual activity of the enzymes, which along with a small concentration of dissolved oxygen could cause the degradation of the anthocyanins. Moreover, HP treatment at moderate temperatures promotes the extractability of coloured pigments and increases the polyphenol content. The results confirm the potentiality of the HP process for the treatment of products rich in thermolable and nutraceutical compounds.