3D cell cultures are increasingly being used in a variety of contexts – including for drug discovery, disease modelling, and tissue engineering – because they offer the potential to increase physiological relevance compared to traditional monolayer cultures, while simultaneously also reducing cost and time compared to in vivo models. Taking a cue from nature, researchers often create 3D cell cultures using hydrogels which can closely mimic the extracellular matrix that most mammalian cells are surrounded by in vivo. However, aside from the collective physical 3D arrangement itself, the physiology of the culture depends highly on the microenvironment, which is defined by the 3D cell culture shape and the complex combination of biochemical, biophysical and biomechanical stimuli. Microfluidic devices offer researchers the tantalizing opportunity to precisely define and influence this microenvironment. Furthermore, they additionally allow for integration of external functional components for active stimulation and monitoring of cultured cells. Pushing for ever-more-realistic culture conditions has, however, increased the complexity that is required of these microfluidic culture systems, which makes their fabrication more difficult. In this regard, 3D printing is becoming an increasingly popular solution, since it offers researchers not only the ability to fabricate highly complex structures but also to benefit from rapid prototyping and customization of existing designs. This review discusses common challenges that researchers face today when integrating hydrogel embedded cells into 3D-printed microfluidic cell culture devices, and seeks to offer a comprehensive overview of recent advancements aimed at addressing these challenges.