This work presents a comprehensive study on the effects of the Friction-based Injection Clinching Joining (F-ICJ) process on the microstructure and local properties of the stake head. The manuscript evaluates the consequences on the quasi-static mechanical performance of hybrid joints of amorphous polyetherimide (PEI) with aluminium AA6082. Through an overlay of microhardness map on a cross-polarized transmitted-light optical microscopy (CP-TLOM) image, two lower-strength microstructural zones in the PEI stake head were observed: a plastically-deformed zone (PDZ) and a thermo-mechanically-affected zone (PTMAZ). When compared to the base material, PDZ and PTMAZ have a reduction of 12%–16% and 8%–12%, respectively, in local mechanical properties. The reduced local strength was associated with distinct volumes of loosely packed PEI chains with unsteady chain conformation and thus larger free volume in the affected regions. The mechanical strength reduction is reversible through physical aging by thermal annealing the joints, which additionally shows that process-induced thermomechanical degradation of PEI by chain scission, as evidenced by size exclusion chromatography (SEC) analysis, does not appear to affect local mechanical strength. An evaluation of typical loading regimes of staked joints in lap shear (average ultimate force of 1419 ± 43 N) and cross tensile (average ultimate force of 430 ± 44 N) testing indicates that the process-induced changes of PEI do not compromise the global mechanical performance of such a structure. These findings provide a better understanding of the relationships between processing, microstructure, and properties for further F-ICJ process optimization.