The APOE ε4 allele was originally reported to contribute to risk of Alzheimer's disease (AD) in women, yet male and female AD patient-derived data are routinely pooled. Histopathological hallmarks of AD include neurofibrillary tangles centered on hyperphosphorylated Tau and plaques composed of the β-amyloid (Aβ) peptide that is derived by sequential secretase-mediated cleavage of the Amyloid Protein Precursor (APP). We chose to examine profiles of Aβ(1-40), Aβ(1-42), and N-truncated (i.e., p3-related) fragments in the plaque-associated fraction of autopsied cortical and corresponding hippocampal samples from donors with a diagnosis of early-onset (EOAD) and late-onset (LOAD) AD. Levels of Aβ(1-40), Aβ(1-42), and the p3 fragment-enriched pool were increased in EOAD and LOAD samples, and correlated well within -but not between- regions. Counterintuitively, these increases were similar regardless of the AD donor's APOE ε4 status. Focusing on the donor's sex and APOE ε4 status as nominal variables (i.e., omitting diagnosis from the stratification) revealed that increases in Aβ peptides were specific to female carriers of the ε4 allele and correlated with the proportional expression of BACE1/β-secretase and ADAM10/α-secretase in the cortex and with nicastrin (γ-secretase) expression in the hippocampus. These data preliminarily support the possibility that AD follows distinct amyloidogenic processes in males and females, and that the APOE ε4 allele exerts a major influence on the disease process, particularly in women. This knowledge could significantly impact the (re)interpretation of unsuccessful outcomes of clinical interventions targeting either Aβ peptides directly or the secretases implicated in APP processing.