Time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used to analyze poly(ether ether ketone) (PEEK) based membranes. PEEK membranes have been shown to be effective in the separation of CO2 from flue gases (post-combustion technique). The PEEK membranes were synthesized using novel aromatic ether-ketone linkages inspired by PEEK with polymeric backbone bistriflimide [Tf2N]− counterions. One of the keys to advancing this technology is developing membranes that are selective and permeable toward CO2, in which PEEK based membranes have been shown to be. Furthermore, the compatibility between various water lean solvents also needs to be investigated. Surface analytical techniques such as x-ray photoelectron spectroscopy and ToF-SIMS are useful for investigating chemical changes between membranes. Herein, we present ToF-SIMS data obtained in the negative ion mode for four different PEEK membranes designed for use in CO2 capture systems. Positive ion mode spectra are reported in Paper I.