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The convective injection and subsequent fate of the peroxides H2O2 and CH3OOH in the upper troposphere is investigated using aircraft observations from the NASA Pacific Exploratory Mission‐Tropics A (PEM‐Tropics A) over the South Pacific up to 12 km altitude. Fresh convective outflow is identified by high CH3I concentrations; CH3I is an excellent tracer of marine convection because of its relatively uniform marine boundary layer concentration, relatively well‐defined atmospheric lifetime against photolysis, and high sensitivity of measurement. We find that mixing ratios of CH3OOH in convective outflow at 8–12 km altitude are enhanced on average by a factor of 6 relative to background, while mixing ratios of H2O2 are enhanced by less than a factor of 2. The scavenging efficiency of H2O2 in the precipitation associated with deep convection is estimated to be 55–70%. Scavenging of CH3OOH is negligible. Photolysis of convected peroxides is a major source of the HOx radical family (OH + peroxy radicals) in convective outflow. The timescale for decay of the convective enhancement of peroxides in the upper troposphere is determined using CH3I as a chemical clock and is interpreted using photochemical model calculations. Decline of CH3OOH takes place on a timescale of a 1–2 days, but the resulting HOx converts to H2O2, so H2O2 mixing ratios show no decline for ∼5 days following a convective event. The perturbation to HOx at 8–12 km altitude from deep convective injection of peroxides decays on a timescale of 2–3 days for the PEM‐Tropics A conditions.