Over the last decade, a multitude of synthesis strategies has been reported for the production of high-quality nanoparticles. Wet-chemical methods are generally the most efficient synthesis procedures since high control of crystallinity and physicochemical properties can be achieved. However, a number of challenges remain from inadequate reaction control during the nanocrystallization process; specifically variability, selectivity, scalability and safety. These shortcomings complicate the synthesis, make it difficult to obtain a uniform product with desired properties, and present serious limitations for scaling the production of colloidal nanocrystals from academic studies to industrial applications. Continuous flow reactors based on microfluidic principles offer potential solutions and advantages. The reproducibility of reaction conditions in microfluidics and therefore product quality have proved to exceed those obtained by batch processing. Considering that in nanoparticles' production not only is it crucial to control the particle size distribution, but also the shape and chemical composition, this review presents an overview of the current state-of-the-art in synthesis of anisotropic and faceted nanostructures by using microfluidics techniques. The review surveys the available tools that enable shape and chemical control, including secondary growth methods, active segmented flow, and photoinduced shape conversion. In addition, emphasis is placed on the available approaches developed to tune the structure and chemical composition of nanomaterials in order to produce complex heterostructures in a continuous and reproducible fashion.