Programmed cell death (PCD) in lateral root caps (LRC) is crucial for maintaining root cap functionality. Endoplasmic reticulum (ER) bodies play important roles in plant immunity and PCD. However, the distribution of ER bodies and their communication with vacuoles in the LRC remains elusive. Toyooka et al. now provide insight into the organization of ER bodies in Arabidopsis LRC cells and on the transportation mechanism of β-glucosidases from ER bodies to vacuoles in LRCs, using wide-region and high-resolution electron microscopy, high-pressure freezing/freeze-substitution (HPF/FS), and correlative light and electron microscopy (CLEM) techniques. This work lays the foundation for understanding both the mechanism of PCD and the protective role of β-glucosidases in LRC cells.