Challenges related to the direct incorporation of volatile antimicrobial compounds into packaging materials were effectively addressed through the use of β-cyclodextrin (βCD) for encapsulation. This research investigated the factors influencing the encapsulation process through the application of two preparation techniques (i.e., co-precipitation, kneading) and two guest compounds (i.e., linalool, eugenyl acetate). The results demonstrated effective encapsulation as evidenced by conformational analysis, which included Fourier-transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), and thermogravimetric analysis (TGA) along with quantitative measurements, encapsulation efficiency (EE%) and release kinetics. The analysis collectively confirmed the encapsulation process by demonstrating comparable absorbance peaks and transition temperatures to native βCD, shifts in the water peak, the absence of guest compound peaks, and altered degradation temperatures. FTIR results indicated that co-precipitation demonstrated greater effectiveness for stable encapsulation, notably improving the thermal stability of eugenyl acetate with significantly (p < 0.05) elevated decomposition temperatures (318 °C) and enhancing the encapsulation efficiency of linalool by 24.2%. Regarding release kinetics, co-precipitation samples exhibited a controlled and steady release, reaching equilibrium for linalool/βCD on day 7 (37 mg/L) and eugenyl acetate/βCD on day 10 (70 mg/L). In contrast, kneading samples resulted in an uncontrolled release pattern for linalool/βCD, characterized by a bursting effect (3292 mg/L on day 1) while eugenyl acetate/βCD never reached equilibrium. The findings highlight the interplay between the guest compound and the preparation methods, indicating that optimized inclusion complexes can function as active additives to enhance the preservation of fresh produce (i.e., cherry tomatoes).