Protein misfolding leads to the formation of amyloid fibrils, which presence is characterized for many serious diseases affecting millions of people worldwide. In the presented study we used, for the first time, magnetooptical (MO) methods such as Faraday and Cotton-Mouton effects (FE and CME respectively) to monitor the aggregation processes of one of the most studied peptides, amyloid β1-40 (Aβ1-40) which is associated with Alzheimer’s disease. Through the anisotropy of optical polarizability and magnetic susceptibility, CME is very sensitive to the shape of the studied species, which allows us to monitor their changes. The impact of incubation time (up to 40 days) and temperature (8, 23, 36 °C) on the aggregation of Aβ1-40 was evaluated by the measured coefficients that describe both effects. CME is found more suitable for monitoring protein aggregation than FE. Formation of Aβ1-40 fibrils and kinetic profile was also confirmed using the Thioflavin T fluorescence assay. Furthermore, CME was successfully used to demonstrate the self-assembly of phenylalanine, which is recognized as the crucial amino acid in the aggregation process of Aβ1-40. Our observations demonstrate the possible role of π-π interaction of aromatic rings in the self-assembly of amyloid fibrils.