The present work reports a study aimed at investigating the recovery and the upgrade of tomato processing residues through the preparation of innovative green composites based on tomato peels (TPs) and natural halloysite nanotubes (HNTs) loaded with carvacrol, as a natural antibacterial agent. The loading of carvacrol into HNTs was successfully achieved through a simple procedure that does not involve any chemical modifications of HNTs. Composite films with different amount of HNTs (i.e., 2.5, 5, 10, 20%wt) were prepared using mechanical milling in presence of water, followed by solvent casting method. The structural organization and the main physical properties of the obtained bio-based active composites have been deeply investigated. In particular, thermal and mechanical properties along with the films’ interaction with water vapor were assessed and then correlated to the filler loading. Results show that the thermal behaviour of bio-composites improves with the filler loading. Conversely, the mechanical properties get worse, especially at higher loading, due to the poor interaction between HNTs and matrix. The presence of hydrophilic HNTs was found to not dramatically increase the degree of hydrophilicity of the of the materials, most likely due to the presence of hydrophobic carvacrol that acts as an hydrophobic coating for HNTs. The release of carvacrol was also analyzed. Results show that the obtained composites exhibit a long-term release of the antimicrobial agent, which suggests them to be promising candidate materials for food packaging application.