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The PAM-2000 portable chlorophyll fluorometer represents one of the first commercially available instruments utilizing the Pulse Amplitude Modulation (PAM) measurement principle, and has become a widely used platform for measuring chlorophyll fluorescence in a wide range of study systems. In this paper, we describe a new method for externally driving and gathering data from the PAM-2000, a method that allows the user to execute a pre-defined user run (or runs) and capture (1) rapid induction kinetics (at 2 ms frequency) during all saturating pulses, (2) measures of F, F-o, F-o’, F-m, and F-m’ associated with those same pulses, and (3) changes in fluorescence F at user-defined intervals between pulses, for the entire user run, with all data compressed into a single, manageable data logger file. Practically, the method makes possible, for example, a post-hoc evaluation of the appropriateness of saturation pulse lengths and intensities during a user run. More importantly it captures, during entire user runs, the varied information contained in slow changes in fluorescence between saturating pulses, as well as rapid induction kinetics, quenching coefficients and quantum yields all gathered simultaneously from all saturating flashes.