This study explores the antioxidant, anti-inflammatory, and anticholinesterase properties of extracts from the natural plant Scorzonera ketzkhowelii for the first time. Additionally, it focuses on isolating phenolic compounds from the ethyl acetate sub-extract, elucidating their structures, and investigating their in-silico bioactivities. Twelve phenolic compounds were isolated and characterized from the ethyl acetate sub-extracts, including hydrangenol (1), 4-hydroxybenzaldehyde (2), luteolin (3), esculin (4), 3-O-caffeoylquinic acid ethyl ester (5), 3-O-caffeoylquinic acid methyl ester (6), kaempferol 3-O-β-glucopyranoside (7), quercetin 3-O-α-arabinopyranoside (8), 3,5-di-O-caffeoylquinic acid ethyl ester (9), thunberginol F 7-O-β-D-glucopyranoside (10), hydrangeic acid 4′-O-β-D-glucopyranoside (11), and 3-O-caffeoylquinic acid (12). The ethyl acetate sub-extracts from both aerial and subaerial parts demonstrated exceptional radical scavenging activity. Moreover, all fractions exhibited potent inhibition against COX-I and COX-II enzymes, with notable inhibitory effects observed in the ethyl acetate and dichloromethane sub-extracts against AChE. Additionally, the inhibitory effects of these compounds were assessed against various biological targets, including TNFα, COX-I, COX-II, human CYP450, and hAChE, through molecular docking studies. According to the molecular docking and dynamics studies, compound 9 emerged as particularly noteworthy across all complexes, exhibiting stable binding modes and promising interactions with key residues involved in inhibition.