As one of Earth's most productive marine ecosystems, the Peruvian Upwelling System transports large amounts of biogenic matter from the surface to the deep ocean. Whilst particle sinking velocity is a key factor controlling the biological pump, thereby affecting carbon sequestration and oxygen-depletion, it has not yet been measured in this system. During a 50-day mesocosm experiment in the surface waters off the coast of Peru, we regularly measured particle sinking velocities and their biogeochemical and physical drivers. We further characterized the general properties of sinking matter (sampling depth: 17 m) under different phytoplankton communities and nutritional states. This dataset contains mean velocities of sinking particles as well as their median size, compactness and shape. We further included the particulate organic carbon flux, the sinking matter nitrogen to phosphorus ratio and the relative contribution of opal and particulate inorganic carbon to the total flux. The particle flux characteristics are complemented by measurements of chlorophyll a concentration in the water column and the relative contribution of diatoms to total chlorophyll a.