Efforts to tap into the broad antimicrobial, insecticidal, and antioxidant activities of essential oils (EOs) are limited due to their strong odor and susceptibility to light and oxidation. Encapsulation of EOs and subsequent drying overcome these limitations and extend their applications. This study characterized freeze-dried (lyophilized) emulsions of eugenol (EU) and thymol (TY) EOs, encapsulated by chemically unmodified cellulose, a sustainable and low-cost resource. High-resolution scanning electron microscopy showed successful lyophilization. While the observed “flake-like” structure of the powders differed significantly from that of the emulsified microcapsules, useful properties were retained. Fourier transform infrared spectroscopy confirmed the presence of EOs in their corresponding powders and thermo-gravimetric analysis demonstrated high encapsulation efficiency (87–88%), improved thermal stability and resistance to evaporation, and slow EO release rates in comparison to their free forms. The lightweight and low-cost cellulose encapsulation, together with the results showing retained properties of the dried powder, enable the use of EOs in applications requiring high temperatures, such as EO incorporation into polymer films, that can be used to protect agricultural crops from microbial infections.