This study aimed to investigate the behavior of smart bilayer films under various temperature and relative humidity (RH). Smart bilayer films were fabricated using sodium alginate with incorporated butterfly pea anthocyanin and agar containing catechin–lysozyme. Cellulose nanospheres were added at concentrations of 0% and 10% w/w of the film and subjected to test at 4 °C and 25 °C, considering different RHs (0%, 50%, and 80%). The results showed that RH had a greater impact on the mechanical properties than temperature, leading to a decrease in tensile strength and an increase in elongation at break with higher RH. The films displayed increased strength but reduced flexibility at low temperatures. Oxygen permeability was negatively affected by increasing RH, while water vapor barrier properties were better at 25 °C than at 4 °C. In terms of color stability, the temperature played a more important role, with both types of smart bilayer films retaining their color stability throughout 14-day storage at 4 °C, even maintaining their ability to change color with pH. However, the films stored at 25 °C exhibited lower color stability and showed potential for color change with varying pH levels, but with lower intensity. The findings of this study demonstrate the significant impact of temperature and RH on the functional properties of smart bilayer films, with and without the addition of cellulose nanospheres. Such smart bilayer films have great potential for various applications, particularly in food packaging, where maintaining color, mechanical, and barrier properties under varying environmental conditions is crucial.