Trafficking of proteins and lipids within the plant endomembrane system is essential to support cellular functions and is subject to rigorous regulation. Despite this seemingly strict regulation, endomembrane trafficking needs to be dynamically adjusted to ever-changing internal and environmental stimuli, while maintaining cellular integrity. Although often overlooked, the versatile second messenger Ca(2+) is intimately connected to several endomembrane-associated processes. Here, we discuss the impact of electrostatic interactions between Ca(2+) and anionic phospholipids on endomembrane trafficking, and illustrate the direct role of Ca(2+) sensing proteins in regulating endomembrane trafficking and membrane integrity preservation. Moreover, we discuss how Ca(2+) can control protein sorting within the plant endomembrane system. We thus highlight Ca(2+) signaling as a versatile mechanism by which numerous signals are integrated into plant endomembrane trafficking dynamics.