In microsystems technology, passivation layers are generally required to protect micro devices and functional elements against environmental impact, particularly against corrosion, thus increasing reliability and lifetime to acceptable values. In this work, the use of sputter-deposited aluminium oxide and aluminium nitride thin films on flexible polyimide foils was investigated, aiming at the protection of flow sensitive elements. Due to a high defect density located at the interface between the passivation layer and the organic substrate, the adhesion of pure aluminium oxide thin films was found to be poor when applying a combination of mechanical stress (e.g. bombardment with water droplets) and thermal cycling as an accelerated ageing procedure. A bi-layer consisting of aluminium nitride and aluminium oxide, however, shows a defect-free interface to the organic substrate resulting in an enhanced adhesion. In addition, no structural failure can be detected after applying the aging procedure, making this bi-layer approach well suited for the targeted application.