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We demonstrate a novel shot-to-shot acquisition method for optical pump-keV electron energy probe in ultrafast scattering experiments. We integrate a phase-locked acquisition scheme at a repetition rate of 20 kHz in a conventional ultrafast electron diffraction setup. We proceed to a full characterization of the noise level in different configurations and for realistic scenarios. The shot-to-shot acquisition improves the signal-to-noise ratio by one order of magnitude and can be readily implemented in other high-repetition-rate electron diffraction and spectroscopy setups.