Understanding the microstructure of agrifood products is key for obtaining stable products and getting leads for further innovations. The current presentation will address opportunities and challenges in microstructure research, reviewing current methodologies in light microscopy, laser microscopy, and electron microscopy. Often, combinations of different types of microscopy provide the best insight in product structure. There will be special emphasis on how to efficiently tackle microstructure research questions and how to find the best combination of methodologies. Aim of this contribution is to guide the audience in the complex world of microscopy and microstructure research, reviewing proven workflows and methodologies.