The development of new sensitive methods for the detailed collection of conformational and morphological information about amyloids is crucial for the elucidation of critical questions regarding aggregation processes in neurodegenerative diseases. The combined approach of two-photon and time-resolved fluorescence spectroscopy described in this report interrogates the early conformational dynamics seen in soluble oligomers of amyloid-β(1-42). Concentration-dependent aggregation studies using two-photon absorption show enhanced sensitivity toward conformational changes taking place in the secondary structure of the amyloid peptide as aggregation proceeds. Fluorescence lifetimes and changes in anisotropy values indicate Förster-type energy transfer occurring as a function of aggregation state. The sensitivity of our two-photon methodology is compared to that of circular dichroism (CD) spectroscopy, and the results indicate that the two-photon absorption cross-section method exhibits superior sensitivity. A theoretical model is developed that, together with electronic structure calculations, explains the change in cross section as a function of aggregation in terms of interacting transition dipoles for aggregates showing stacked or parallel structures. This suggests that the two-photon method provides a sensitive alternative to CD spectroscopy while avoiding many of the inherent challenges particular to CD data collection. The implication of this finding is significant, as it indicates that a two-photon-based technique used in conjunction with time-resolved fluorescence might be able to reveal answers to conformational questions about amyloid-β(1-42) that are presently inaccessible with other techniques.