Bearing in mind the centuries-old traditional use of chamomile, but also the increasing demand for its products in modern industry, oriented toward sustainable development, there are increasing efforts for the efficient extraction of high-value compounds of this plant, as well as obtaining its products with added value. With that goal, conventional and contemporary separation techniques were applied in this work. Both hydrodistillation processes (HD), conducted in a traditional manner and coupled with microwave irradiation (MWHD), were used for essential oil isolation. In parallel with those procedures, chamomile lipophilic extracts were obtained by Soxhlet extraction applying organic solvents and using supercritical fluid extraction as a greener approach. The obtained extracts and essential oils were characterized in terms of chemical composition (GC analysis, contents of total phenolics and flavonoids) and biological potential. GC analysis revealed that oxygenated sesquiterpenes and non-terpene compounds were the dominant compounds. α-Bisabolol oxide A (29.71–34.41%) and α-bisabolol oxide B (21.06–25.83%) were the most abundant individual components in samples obtained by distillation while in supercritical and Soxhlet extracts, major compounds were α-bisabolol oxide A and pentacosane. The biological potential of essential oils and extracts was tested by applying a set of analyzes to estimate the inhibition of biologically important enzymes (amylase, glucosidase, acetylcholinesterase, butyrylcholinesterase, tyrosinase) and antioxidant capacity (DPPH, ABTS, CUPRAC, FRAP, chelating and total antioxidant capacity). The results suggested essential oils as better antioxidants, while the extracts were proven to be better inhibitors of the tested enzymes. Principal Component Analysis was conducted using the experimental results of the composition of extracts and EOs of chamomile obtained by different separation techniques, showing clear discrimination between methods applied in correlation with the chemical profile. Molecular docking was applied for the identification of the main active principles present in the essential oil, among which α-bisabolol-oxide B (cp3) showed a higher affinity for tyrosinase.