Calcium carbonate (CaCO3) is one of the most abundant biominerals that is prevalent in rocks and often used as a structural material in marine animals. Many of these natural CaCO3-based materials display excellent mechanical properties that are difficult to reproduce by man-made counterparts. This difficulty arises from the incomplete understanding of the influence of processing conditions on the structure and composition of CaCO3. To gain a better understanding of the evolution of the structure and composition of amorphous CaCO3 (ACC) particles during early stages, we introduce a new, organic solvent-free method that quenches this process with a high temporal resolution. We produce ACC particles inside small airborne drops that are formed with a microfluidic spray-dryer. These drops dry within 100 ms to 10 s and thereby arrest the formation of CaCO3 particles on that time scale. Using the microfluidic spray-dryer, we demonstrate that the amount of mobile water contained in ACC particles increases with increasing formation time and hence with increasing particle size. As a result of the higher concentration of mobile water, larger particles are less stable against temperature-induced solid-state crystallization and electron beam-induced decomposition than smaller counterparts. The amount of mobile water contained in ACC can be substantially reduced, and hence their kinetic stability against solid-state transformations increased, if certain organic additives, such as poly(acrylic acid) (PAA), are incorporated. These insights might open up new opportunities to fabricate biomimetic CaCO3-based materials with tunable structures and hence with properties that can be adapted to the needs of specific applications.