Pine pollen is widely used in traditional Chinese medicine and has been consumed as a food product for thousands of years. Owing to wind pollination, its pollen grains are composed of a sporoplasmic central cavity along with two empty air sac compartments. While this architectural configuration is evolutionarily optimized for wind dispersal, such features also lend excellent potential for encapsulating materials, especially in the context of preparing sporopollenin exine capsules (SECs). Herein, we systematically evaluated one-pot acid processing methods in order to generate pine pollen SECs that support compound loading. Morphological properties of the SECs were analysed by scanning electron microscopy (SEM) and dynamic imaging particle analysis (DIPA), and protein removal was evaluated by CHN elemental analysis and confocal laser scanning microscopy (CLSM). It was identified that 5-h acidolysis with 85% w/v phosphoric acid at 70 °C yielded an optimal balance of high protein removal and preservation of microcapsule architecture, while other processing methods were also feasible with an additional enzymatic step. Importantly, the loading efficiency of the pine pollen SECs was three times greater than that of natural pine pollen, highlighting their potential for microencapsulation. Taken together, our findings outline a successful strategy to prepare intact pine pollen SECs and demonstrate for the first time that SECs can be prepared from multi-compartmental pollen capsules, opening the door to streamlined processing approaches to utilize pine pollen microcapsules in industrial applications.