Polymeric particles have attracted vast attention for use in various fields, especially as drug carriers and cosmetics, due to their excellent ability to protect active ingredients from the environment until reaching a target site. However, these materials are commonly produced from conventional synthetic polymers, which impose adverse effects on the environment due to their nondegradable nature, leading to waste accumulation and pollution in the ecosystem. This work aims to utilize naturally occurring Lycopodium clavatum spores to encapsulate sacha inchi oil (SIO), which contains active compounds with antioxidant activity, by applying a facile passive loading/solvent diffusion-assisted method. Sequential chemical treatments by acetone, potassium hydroxide, and phosphoric acid were employed to remove native biomolecules from the spores before encapsulation effectively. These are mild and facile processes compared to other synthetic polymeric materials. Scanning electron microscopy and Fourier-transform infrared spectroscopy revealed the clean, intact, and ready-to-use microcapsule spores. After the treatments, the structural morphology of the treated spores remained significantly unchanged compared to the untreated counterparts. With an oil/spore ratio of 0.75:1.00