Beer is a complex aqueous mixture of organic and inorganic compounds, such as carbohydrates obtained from barley or wheat malts, hops and yeast, ethanol, proteins, vitamins, and minerals. Phenols and their derivatives obtained by chemical interactions with biogenic amines, together superior alcohols and amino acids, are the other compounds present in minor proportions in beer, Phenolic components possess high antioxidant activities, and regulate the oxidative stability of beer, although bitterness of this beverage originates from hops. Since these antioxidants can produce beneficial effects on the human health after consumption, it is challenging to have in hand the molecular profiles of beers, in order to investigate their contents in bioactive compounds. Today, a significant number of small producers have strongly invested in craft beers, produced by using different hop blends, starting materials that are rich in phenolic antioxidants. The present work discloses an instrumental analytical method which enables the rapid obtainment of the molecular profiling of craft beers, with the assistance of selective extractions made by using multi-walled carbon nanotubes (MWCNTs). In this investigation, high-resolution 1H NMR, and LDMS and MS/MS analysis were applied for the “beeromic” analysis of a craft beer brewed in Calabria (the Southern part of Italy). The spectral data, confirmed that this kind of beer predominantly contains the hop bitter metabolites humolones and lupulones, also highlighting the presence of phenols and phenolamides which are known for their bioactivity against cancer. A profile of the principal volatile hop components was also obtained by GC-MS.