Epitaxially stacking colloidal quantum dots in nanowires offers a route to selective passivation of defective facets while simultaneously enabling charge transfer to molecular adsorbates – features that must be combined to achieve high-efficiency photocatalysts. This requires dynamical switching of precursors to grow, alternatingly, the quantum dots and nanowires – something not readily implemented in conventional flask-based solution chemistry. Here we report pulsed axial epitaxy, a growth mode that enables the stacking of multiple CdS quantum dots in ZnS nanowires. The approach relies on the energy difference of incorporating these semiconductor atoms into the host catalyst, which determines the nucleation sequence at the catalyst-nanowire interface. This flexible synthetic strategy allows precise modulation of quantum dot size, number, spacing, and crystal phase. The facet-selective passivation of quantum dots in nanowires opens a pathway to photocatalyst engineering: we report photocatalysts that exhibit an order-of-magnitude higher photocatalytic hydrogen evolution rates than do plain CdS quantum dots.