One of the major hallmarks of Alzheimer’s disease (AD) pathology is the formation of extracellular amyloid β (Aβ) plaques. While Aβ has been suggested to be critical in inducing and, potentially, driving the disease, the molecular basis of AD pathogenesis is still under debate. Extracellular Aβ plaque pathology manifests itself upon aggregation of distinct Aβ peptides, resulting in morphologically different plaque morphotypes, including mainly diffuse and cored senile plaques. As plaque pathology precipitates long before any clinical symptoms occur, targeting the Aβ aggregation processes provides a promising target for early interventions. However, the chain of events of when, where and what Aβ species aggregate and form plaques remains unclear. The aim of this study was to investigate the potential of matrix‐assisted laser desorption/ionization imaging mass spectrometry as a tool to study the evolving pathology in transgenic mouse models for AD. To that end, we used an emerging, chemical imaging modality – matrix‐assisted laser desorption/ionization imaging mass spectrometry – that allows for delineating Aβ aggregation with specificity at the single plaque level. We identified that plaque formation occurs first in cortical regions and that these younger plaques contain higher levels of 42 amino acid‐long Aβ (Aβ1–42). Plaque maturation was found to be characterized by a relative increase in deposition of Aβ1–40, which was associated with the appearance of a cored morphology for those plaques. Finally, other C‐terminally truncated Aβ species (Aβ1–38 and Aβ1–39) exhibited a similar aggregation pattern as Aβ1–40, suggesting that these species have similar aggregation characteristics. These results suggest that initial plaque formation is seeded by Aβ1–42; a process that is followed by plaque maturation upon deposition of Aβ1–40 as well as deposition of other C‐terminally modified Aβ species.