Ambient Backscatter Communication (AmBC) enables battery-free IoT devices but is highly vulnerable to eavesdropping due to its broadcast nature and limited processing capabilities. This paper proposes a dual-antenna architecture to enhance physical layer security in AmBC-based IoT systems. The design combines a microstrip patch antenna array for efficient ambient signal reception and energy harvesting with a directional quasi-Yagi-Uda antenna for secure transmission. Antenna parameters are optimized using multi-objective genetic algorithm (MOGA) and multi-objective particle swarm optimization (MOPSO), applied separately to analyze their effectiveness and trade-offs. The proposed dual-antenna system was designed and electromagnetically evaluated using CST Studio Suite, where key parameters such as S11, VSWR, gain, and radiation patterns were obtained. The antenna optimization and secrecy capacity analysis were subsequently performed in MATLAB, enabling comparative evaluation between baseline and optimized designs using MOGA and MOPSO approaches. Results show improved directional gain, reduced side-lobe levels, and enhanced secrecy capacity compared to baseline antenna designs, with clear performance differences observed between MOGA and MOPSO optimized solutions. These findings demonstrate that optimized directional antennas provide a practical and energy-efficient approach for strengthening physical layer security in AmBC-enabled IoT environments.