Quenching and annnealing of polyetheretherketone (PEEK) was performed to study the changes in its physical properties and its interfacial shear strength with AS4 graphite fibers. Physical and mechanical properties of the PEEK matrix were studied using Differential Scanning Calorimetry (DSC) and tensile tests. Plasma polymer deposition of ethylene and ammonia gas mixtures was carried out on the fiber surface to improve the graphite fiber/PEEK matrix adhesion. The adhesion of treated fibers to PEEK was studied using single fiber composite (SFC) tests. Graphite fiber strength were not affected by the plasma polymer deposition process. The SFC tests showed that the interfacial shear strength (IFSS) between graphite fibers treated with ammonia/ethylene gas mixture plasma and PEEK increased by about 84%. However, 100% ethylene plasma deposition, which was strongly hydrocarbon in nature, had no effect an the IFSS. It was found that annealing increases the maximum yield stress, but has no effect on the initial modulus of PEEK. The effect of heat treatment time on the interface strength was also studied. The interface strength increased by a factor of two after the heat treatment.