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<p>The eastern boundary region of the southeastern Pacific Ocean hosts one of the world's most dynamic and productive upwelling systems with an associated oxygen minimum zone (OMZ). The variability in downward export fluxes in this region, with strongly varying surface productivity, upwelling intensities and water column oxygen content, is however poorly understood. Thorium-234 (<span class="inline-formula">²³⁴Th</span>) is a powerful tracer to study the dynamics of export fluxes of carbon and other elements, yet intense advection and diffusion in nearshore environments impact the assessment of depth-integrated <span class="inline-formula">²³⁴Th</span> fluxes when not properly evaluated. Here we use vessel-mounted acoustic Doppler current profiler (VmADCP) current velocities, satellite wind speed and in situ microstructure measurements to determine the magnitude of advective and diffusive fluxes over the entire <span class="inline-formula">²³⁴Th</span> flux budget at 25 stations from 11 to 16<span class="inline-formula">^∘</span>&thinsp;S in the Peruvian OMZ. Contrary to findings along the GEOTRACES P16 eastern section, our results showed that weak surface wind speed during our cruises induced low upwelling rates and minimal upwelled <span class="inline-formula">²³⁴Th</span> fluxes, whereas vertical diffusive <span class="inline-formula">²³⁴Th</span> fluxes were important only at a few shallow shelf stations. Horizontal advective and diffusive <span class="inline-formula">²³⁴Th</span> fluxes were negligible because of small alongshore <span class="inline-formula">²³⁴Th</span> gradients. Our data indicated a poor correlation between seawater <span class="inline-formula">²³⁸U</span> activity and salinity. Assuming a linear relationship between the two would lead to significant underestimations of the total <span class="inline-formula">²³⁴Th</span> flux by up to 40&thinsp;% in our study. Proper evaluation of both physical transport and variability in <span class="inline-formula">²³⁸U</span> activity is thus crucial in coastal <span class="inline-formula">²³⁴Th</span> flux studies. Finally, we showed large temporal variations on <span class="inline-formula">²³⁴Th</span> residence times across the Peruvian upwelling zone and cautioned future carbon export studies to take these temporal variabilities into consideration while evaluating carbon export efficiency.</p>