By exposing catalytic nanoparticles to reactive source gases, nanowires can be grown with excellent control over length, diameter, crystal structure and composition. Here we discuss the degree to which this vapour-liquid-solid growth mechanism can be augmented by “programming” a sequence of reactions in the catalyst. Our aim is to produce complex structures in which quantum dots and quantum wells of precise dimensions are incorporated into single nanowires. We supply different species to nanowire catalysts, either as reactive gases or by evaporation, triggering the formation of new phases that become incorporated into the nanowires as they grow. In situ transmission electron microscopy allows us to view this process, identify phases and measure kinetics. As an example, we discuss the formation of silicide quantum dots within Si nanowires. Supplying metals such as Co and Ni to catalysts composed of liquid AuSi results in the formation of faceted silicide nanocrystals. These floating nanocrystals subsequently attach at the AuSi/Si interface. Further growth of Si incorporates these quantum dots into the nanowire. We discuss the generality of this phenomenon and the control of silicide structure and dimensions. The formation of narrow quantum wells, such as Ge layers within Si nanowires, can also benefit from understanding the sequential changes in the catalyst. We describe the relationship between catalyst properties and quantum well compositional abruptness, strain and stability. We finally consider the possibilities of combining quantum dots and quantum wells in single nanowires. We suggest that control of reaction pathways within the catalyst provides exciting opportunities for the growth of complex nanostructures.