The 4-subunit intramembrane protease complex γ-secretase cleaves many substrates including fragments of the β-amyloid precursor protein (APP), leading to formation of Aβ peptides, and Notch. Mutations in APP and the catalytic subunit of γ-secretase, presenilin, cause familial Alzheimer's disease (fAD). Mutations are assumed to change the substrate-binding and cleavage and thereby the Aβ formed. Whereas a wild-type structure of substrate-bound γ-secretase became recently available from cryogenic electron microscopy (6IYC), the structure and dynamics of mutant proteins remain obscure. Here, we studied five prominent mutants of substrate-bound γ-secretase by explicit all-atom molecular dynamics in a phospholipid membrane model at physiological temperature using the experimental structure as template: The presenilin 1 mutants E280A, G384A, A434C, and L435F and the V717I mutant of APP. Our structures and dynamics provide the first atomic detail into how fAD-causing mutations affect substrate binding to γ-secretase. The pathogenic mutations tend to increase the space and variability in the substrate binding site, as seen e.g. from the distance from catalytic aspartate to substrate cleavage sites. We suggest that we have identified the molecular cause of the "imprecise cleavage" that leads to two trimming pathways in γ-secretase, consistent with the FIST model, which may rationalize the experimental Aβ42/Aβ40 ratios as a molecular basis for fAD.