Elderberry (Sambucus nigra L.) and linden (Tilia cordata Mill.) flower extracts are known for their pro-healthy properties. Various extraction methods, both conventional (Soxhlet) and advanced (ultrasound assisted extraction, UAE, accelerated solvent extraction, ASE, and matrix solid phase dispersion, MSPD), were applied to obtain ethanol–water extracts from the plants. The biological profiles, the total polyphenol content (TPC) and total flavonoid content (TFC) in the extracts were determined spectrophotometrically. Almost 40 compounds were identified in extracts by means of HPLC-MS/MS. The contents of the chosen phenolic acids (chlorogenic, p-coumaric, protocatechuic, and gallic) and flavonoids (rutin, catechin, quercetin, kaempferol, apigenin, and naringenin) were determined by HPLC-DAD. It was observed that the elderflower extracts contained higher levels of the compounds investigated than did the linden extracts. Chlorogenic acid was the main phenolic acid in the majority of extracts form the elderberry flower, whereas in the linden extracts, it was protocatechuic acid. Nevertheless, rutin was the main component of both plant extracts. The cytotoxicity of the elderberry and linden flower extracts against VERO, FaDu, H1HeLa, and RKO cell lines were subsequently examined. The elderflower extracts exerted no cytotoxicity, whereas linden extracts showed selective cytotoxicity against FaDu and RKO cells with CC50 of 54.35 and 46.27 µg/mL, respectively. The antiviral potential of the extracts against HHV-1, CVB3, and HRV14 were also examined. The results demonstrate antiviral activity against HHV-1, particularly for linden flower extract in concentration of 62.5 µg/mL.