This paper examines the influence of cooling rate after molding on short- and long-term properties of continuous carbon fiber reinforced polyetheretherketone (PEEK). First, changes to matrix structure and internal stress levels resulting from cooling panels at different rates are described for composites of PEEK with AS4 and IM6 fibers. The effects of these changes on short-term properties are illustrated by tension, compression, delamination resistance, and drop weight impact tests and results are compared with published data. Long-term properties are then discussed and results from creep loading, tension-tension fatigue, and Mode I delamination fatigue are presented. Both short- and long-term results indicate that the internal stresses induced during fast cooling are more detrimental to the performance of IM6 carbon fiber/PEEK composites than the changes in matrix structure observed at slow cooling rates.