Maleic anhydride plasma polymers enable amine-containing biomolecules and polymers to be covalently coupled to a surface from an aqueous solution without any intermediate chemistry. The challenge in developing these functionally active plasma polymers lies in determining the optimal deposition conditions for producing a stable, highly active film. Unlike many previous studies that explore highly varied pulsed and continuous wave (CW) deposition conditions, this paper focuses on the comparison of films deposited under the same low nominal power conditions (I W) and compares a range of CW, millisecond, and microsecond pulsing parameters that can be used to produce this power condition. The use of attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) and X-ray photoelectron spectroscopy (XPS) has enabled the quantitative examination of the effects of processing parameters on the chemical functionality of the films. For the first time, the molecular specificity, surface sensitivity, and high mass resolution of time-of-flight static secondary ion mass spectrometry (ToF-SSIMS) has been exploited to compare these films and multivariate analysis techniques used to explore the relationships between plasma processing parameters and surface chemistry. The results of the studies clearly demonstrate that a range of conditions can produce maleic anhydride films, with optimal functionality seen under microsecond pulsing regimes. Critically, the study demonstrates that the tight control and monitoring of the deposition parameters is critical if these films are to be manufactured with optimal functionality, stability, and minimum processing time.