Background: Tomato pomace (TP) is a coproduct generated by the extraction of tomato pulp, and is a potential source of bioactive molecules. In this study, we isolated several fractions from TP and evaluated their biological properties. Materials and Methods: TP was treated by maceration at room temperature with green solvents (ethanol, ethyl acetate, ethanol:water and ethanol:ethyl acetate) or supercritical CO2 (SC-CO2). The extracts were analyzed by HPLC-DAD to determine their composition, and their antioxidant activity was assessed. The potential therapeutic effects of the isolated fractions were assessed in vitro. Results: We identified 30 molecules on chromatography profiles, which revealed an abundance in phenolic acids, carotenoids, flavonoids and tannins, with differences in selectivity according to the solvent and pretreatment used. The highest radical scavenging activities were measured at 64–72% inhibition, corresponding to the ethanol or ethanol:water extracts with the highest polyphenol or flavonoid contents. Carotenoid content was increased by chemical pretreatment, to attain levels of 161 mg β-carotene/g ethyl acetate extract. This level of carotenoids seemed to have anti-inflammatory effects, with an IC50 of 9.3 μg/mL. In terms of anti-diabetic effects, the activities of α-glucosidase and α-amylase were best inhibited by extraction in an ethanol-to-water mixture (50:50). Cytotoxicity in a tumor cell line were highest for SC-CO2 extracts (64.5% inhibition) and for ethanol extracts obtained after the enzymatic pretreatment of TP (37% inhibition). Some extracts also had dose-dependent activity against Zika virus. Conclusions: New fractions obtained from TP with ecocompatible solvents in mild conditions are rich in bioactive molecules. A comparison of the chromatographic profiles of the extracts led to the identification of several key molecules with therapeutic properties. The chemical pretreatment of TP is justified as a mean of increasing the carotenoid content of ethyl acetate fractions, whereas enzymatic pretreatment can increase the antioxidant activity of ethyl acetate fractions and increase the cytotoxicity of ethanol fractions. The SC-CO2 fraction contained a smaller number of metabolites detectable on HPLC, but it had high levels of cytotoxicity and antioxidant activity. Finally, the fractions obtained appeared to be suitable for use to target one or several of the biological activities studied.