Melatonin is involved in the physiological regulation of the β- amyloid precursor protein (βAPP) cleaving secretases which are responsible for generation of the neurotoxic amyloid beta (Aβ) peptide, one of the hallmarks of Alzheimer's disease (AD) pathology. In this study, we aimed to determine the underlying mechanisms of this regulation under pathological conditions. We establish that melatonin prevents Aβ42 -induced down-regulation of a disintegrin and metalloproteinase domain-containing protein 10 (ADAM10) as well as up-regulation of β-site APP-cleaving enzyme 1 (BACE1) and presenilin 1 (PS1) in SH-SY5Y cell cultures. We also demonstrate that the intrinsic mechanisms of the observed effects occurred via regulation of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) and glycogen synthase kinase (GSK)-3β as melatonin reversed Aβ42 -induced up-regulation and nuclear translocation of NF- κBp65 as well as activation of GSK3β via its receptor activation. Furthermore, specific blocking of the NF-κB and GSK3β pathways partially abrogated the Aβ42 -induced reduction in the BACE1 and PS1 levels. In addition, GSK3β blockage affected α-secretase cleavage and modulated nuclear translocation of NF-κB. Importantly, our study for the first time show that peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (Pin1) is a crucial target of melatonin. The compromised levels and/or genetic variation of Pin1 are associated with age dependent tau and Aβ pathologies and neuronal degeneration. Interestingly, melatonin alleviated the Aβ42 -induced reduction of nuclear Pin1 levels and preserved the functional integrity of this isomerase. Our findings illustrate that melatonin attenuates Aβ42 -induced alterations of βAPP-cleaving secretases possibly via the Pin1/ GSK3β / NF-κB pathway. This article is protected by copyright. All rights reserved.