The Amyloid Imaging to Prevent Alzheimer’s Disease (AMYPAD) Prognostic and Natural History Study (PNHS) is an open-label, prospective, multicentre, cohort study linked to a variety of European Parent Cohorts. AMYPAD PNHS aims to improve disease modelling efforts and individualized risk stratification within the context of Alzheimer's disease through the additional collection of amyloid burden using positron emission tomography (PET) imaging. The AMYPAD PNHS dataset integrates information from 10 Parent Cohorts: ALFA+, AMYPAD DPMS, DELCODE, EMIF-AD (60++), EMIF-AD (90+), EPAD LCS, FACEHBI, FPACK, Microbiota, and UCL-2010-412, comprising a total of 3368 participants. Of these, 1620 underwent a baseline amyloid PET, including visual reads and the Centiloid quantification (1476 subjects) among other metrics. Moreover, 888 participants have (at least) one follow-up PET scan, 763 of whom have Centiloid quantification. The participant’s demographic data, clinical outcomes (e.g., cognition), disease biomarkers (imaging and CSF), risk factors (e.g., genetics and environmental), and other relevant variables are included in the dataset. This updated version of the AMYPAD dataset adds computed polygenic risk scores from harmonised genotype array data, a comprehensive set of imaging-derived endophenotypes from various MRIprocessing pipelines and corrections to selected cognition-related scores.