Natural pigment-based pH indicators are promising candidates for intelligent food packaging due to their biocompatibility and distinct color responses. However, their practical application is limited by color stability and functional performance during storage. In this study, pH indicators incorporating betacyanin (Bet-Ind), anthocyanin (Ant-Ind), and phycocyanin (Phy-Ind) were prepared on cellulose filter paper, and their antibacterial activity, moisture absorption, and color stability were evaluated over 12 days under ambient (20 °C), refrigerated (4 °C), and frozen (−18 °C) conditions. Antibacterial assays revealed that all indicators inhibited the growth of Escherichia coli, Bacillus cereus, Listeria monocytogenes, and Staphylococcus aureus. The largest inhibition zone was observed against S. aureus (7 mm), while Phy-Ind exhibited the strongest effect on B. cereus (6 mm) and Ant-Ind showed the highest inhibition against L. monocytogenes (5.67 mm) (p < 0.05). Moisture absorption of the control filter paper increased from 0.35% to 10.56%, whereas pigment-based indicators demonstrated lower absorption, ranging from 9.12% to 10.09% (p < 0.05). Color stability analysis indicated that total color change (ΔE) was strongly dependent on pigment type and storage temperature. Betacyanin exhibited the highest stability under refrigeration (ΔE ≈ 7), phycocyanin showed minimal color change under freezing (ΔE ≈ 2.24), while anthocyanin displayed the greatest instability (p < 0.05). Overall, the findings highlight that pigment selection and storage conditions are critical factors in enhancing the performance of natural pH indicators for smart food packaging applications.