Hybrid joints consisting of metals and fiber-reinforced polymer composites exhibit highly desirable properties for many lightweight design applications. This study investigates the potential of additively manufactured surface structures for enhancing the bond strength of such joints in comparison to face milled and laser structured surfaces. Titanium samples with different surface structures (as-built surface, groove-, and pin-shaped structures) were manufactured via electron beam melting and joined to carbon fiber-reinforced polyether-ether-ketone (PEEK) via adhesive bonding and thermal direct joining, respectively. Bond strength was evaluated by tensile shear testing. Samples were exposed to salt spray testing for 1000 h for studying bond stability under harsh environmental conditions. The initial tensile shear strengths of the additively manufactured samples were competitive to or in some cases even exceeded the values achieved with laser surface structuring for both investigated joining methods. The most promising results were found for pin-shaped surface structures. However, the hybrid joints with additively manufactured structures tended to be more susceptible to degradation during salt spray exposure. It is concluded that additively manufactured structures can be a viable alternative to laser surface structuring for both adhesive bonding and thermal direct joining of metal-polymer hybrid joints, thus opening up new potentials in lightweight design.