Crustacean larvae have served as distinguished models in the field of Ecological Developmental Biology (“EcoDevo”) for many decades, a discipline that examines how developmental mechanisms and their resulting phenotype depend on the environmental context. A contemporary line of research in EcoDevo aims at gaining insights into the immediate tolerance of organisms and their evolutionary potential to adapt to the changing abiotic and biotic environmental conditions created by anthropogenic climate change. Thus, an EcoDevo perspective may be critical to understand and predict the future of organisms in a changing world. Many decapod crustaceans display a complex life cycle that includes pelagic larvae and, in many subgroups, benthic juvenile–adult stages so that a niche shift occurs during the transition from the larval to the juvenile phase. Already at hatching, the larvae possess a wealth of organ systems, many of which also characterise the adult animals, necessary for autonomously surviving and developing in the plankton and suited to respond adaptively to fluctuations of environmental drivers. They also display a rich behavioural repertoire that allows for responses to environmental key factors such as light, hydrostatic pressure, tidal currents, and temperature. Cells, tissues, and organs are at the basis of larval survival, and as the larvae develop, their organs continue to grow in size and complexity. To study organ development, researchers need a suite of state-of-the-art methods adapted to the usually very small size of the larvae. This review and the companion paper set out to provide an overview of methods to study organogenesis in decapod larvae. This first section focuses on larval rearing, preparation, and fixation, whereas the second describes methods to study cells, tissues, and organs.