Additive manufacturing technologies such as fused filament fabrication (FFF) open many possibilities in terms of product functionality, including the possibility to integrate a sensor in FFF parts to perform structural health monitoring. In this context, embedding fiber Bragg grating (FBG) sensors into 3D-printed polymeric structures for strain or temperature measurements has attracted increasing attention in recent years. Indeed, offering structural health monitoring functionality can optimize the maintenance cost and increase security compared with conventional materials. However, the transmission of strain and temperature between the polymeric matrix and the FBG polymer jacket requires optimal bonding between them. In this work, the two polymers of interest are polyimide (PI) and poly(lactic acid) (PLA) for the FBG jacket and printed polymer, respectively. The current study investigates the influence of different surface treatment methods on the adhesion between a PI film and a plate of PLA, with PLA and PI being incompatible polymers. The adhesion promotion applied to the PI surface relies on cleaning, plasma activation, roughness modification, or the use of adhesive nanocoating. Bilayer samples of PI-PLA are processed by welding PLA against the treated PI by heating, whereas the adhesion between PI and PLA is measured by peel testing. It is observed that the highest adhesion between PI and PLA is achieved by a combination of mechanical abrasion increasing roughness and the use of polydopamine as an adhesive. This finding is discussed based on a synergetic effect between mechanical interlocking and chemical interaction between the two counterfaces.