This study proposes a robust microshell encapsulation system in which a metal-organic membrane (MOM), consisting of phytic acids (PAs) and metal ions, intrinsically prevents the molecular crystal growth of organic crystalline materials (OCMs). To develop this system, OCM-containing oil-in-water (O/W) Pickering emulsions were enveloped with the MOM, in which anionic pulp cellulose nanofiber (PCNF) primers electrostatically captured zinc ions at the O/W interface and chelated with PA, thus producing the MOM with a controlled shell thickness at the micron scale. We ascertained that the MOM formation fills and covers ∼75% of the surface pore size of PCNF films, which enhances the interfacial modulus by 2 orders of magnitude compared to that when treated with bare PCNFs. Through a feasibility test using a series of common OCMs, including ethylhexyl triazone, avobenzone, and ceramide, we demonstrated the excellent ability of our MOM microshell system to stably encapsulate OCMs while retaining their original molecular structures over time. These findings indicate that our MOM-reinforced microshell technology can be applied as a platform to substantially confine the crystal growth of various types of OCMs.