Porous high surface area supramolecules have been widely researched for controlled delivery and chemical stabilization of active molecular species. Metal–organic frameworks (MOFs), a vast category of high surface area microporous compounds, can be tailored to encapsulate specific active molecules, and control their release kinetics in the headspace of a product-package system for treatment and shelf-life extension of various agricultural produce. Hexanal has been widely reported to reduce post-harvest losses due to its antimicrobial, antifungal, ethylene-modulating, and phospholipase D (PLD) inhibiting characteristics. In this work, we synthesized Calcium-Squarate MOF by a quick simple mechanochemical process using bioderived linkers and non-toxic endogenous cations. We herein report the encapsulation of hexanal in Ca-Squarate MOF, and probe the strength of non-covalent host–guest interactions of hexanal encapsulated in the pores. The synthesized MOF crystals were characterized by thermal analysis, infrared spectroscopy, and diffraction studies. We observed approximately 20% encapsulation of hexanal by weight using thermo-gravimetric analysis. The infrared spectroscopy and simulation study supported the formation of hydrogen bonds between H atoms of hexanal and O atoms of the Ca-Squarate MOF with the strongest binding affinity of −3.81 kcal mol−1. Crystals maintained their porous structure and microscale morphologies post-encapsulation, as observed using X-ray diffraction and scanning electron microscopy. These results are encouraging for the potential use of hexanal encapsulated MOFs in active packaging applications.