This study investigates how aluminum oxide (Al₂O₃) coatings deposited by atomic layer deposition (ALD) can improve the surface hydrophobicity and barrier performance of polylactic acid (PLA) films for food packaging applications. An attempt was made to optimize the effect of Al₂O₃ ALD thin films deposited with different thicknesses on the contact angle and barrier properties. In the thickness measurements and characterizations made by FTIR, XPS, and SEM analysis confirmed the successful deposition of the Al₂O₃ ALD film. Surface wettability was assessed via water contact angle (CA) measurements, revealing that Al₂O₃ coatings significantly increased CA from 74.9° (uncoated-PLA) to 98.5° (20 nm-coated-PLA), indicating enhanced hydrophobicity. Bending tests showed that mechanical deformation can reduce hydrophobic performance, highlighting the coating’s sensitivity to physical stress. Notably, the 20 µm thick PLA film coated with 20 nm Al₂O₃ was the most significantly affected by bending, as its contact angle decreased from 98.5° to 86.8°. The Al₂O₃ coating resulted in a notable decrease in the films’ water vapor transmission rate, reducing it from 150.3 g/m²/day to 4.7 g/m²/day. This considerable improvement in barrier properties is expected to contribute to a prolonged shelf life for packaged food products. Overall migration analyses confirmed that Al₂O₃-coated PLA films limited the total residue migration below the regulatory detection limit of 10 mg/dm². However, specific migration analyses indicated that aluminum (Al) release (3.74–11.75 mg/kg) increased with coating thickness and was more pronounced in acidic simulants (3% acetic acid), suggesting chemical interactions between the coating and simulant. Variations in migration behavior were observed depending on PLA substrate type and coating morphology. These findings demonstrate that Al₂O₃ ALD coatings improve the PLA film functional properties but also highlight the need to carefully control coating quality and regulatory compliance in food-contact applications.