The seeds of Aframomum melegueta K. Schum (grains of paradise, Zingiberaceae) are used as a common spice in African countries and a fine condiment in the European cuisine. In this study, we evaluated the phytochemical profile of various seed extracts of A. melegueta as well as their antimicrobial, antioxidant and enzyme inhibitory effects. In total, 25 diarylheptanoids, five gingerol derivatives and nine phenolic/organic acids were tentatively annotated in A. melegueta by liquid chromatography hyphenated with high resolution tandem mass spectrometry (LC-HRMS/MS). A. melegueta showed a moderate inhibitory activity against different human pathogenic microbial strains, with H. pylori the most sensitive microorganism. A strong antioxidant and enzyme inhibitory potential was shown in various radical scavenging, reducing and chelating assays as well as in cholinesterase, tyrosinase and glucosidase assays. Several specialized metabolites from A. melegueta (diarylheptanoids, gingerols) were shown to be directly linked with the investigated antioxidant and enzyme inhibitory activities, as evaluated through the correlation analysis. In addition, two diarylheptanoids (one heptan-3-ol and one heptan-3,5-diol) displayed the strongest binding to acetylcholinesterase (AChE) via multiple H-bonds, a couple of π-π interactions and van der Waals interactions all over the catalytic channel of the enzyme, as evidenced by the molecular docking study. Overall, our work brings new contributions to the phyto-complexity and poly-pharmacology of spices from genus Aframomum than can find future applications in pharmaceutical, nutraceutical or cosmeceutical industry.