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 sampled sedimented material (sampling depth: 17 m) and analyzed the properties of sinking particles using an optical measurement approach. The presented dataset includes sinking velocity, particle size (ESD), compactness (porosity) and shape (aspect ratio) of >100.000 individually measured particles.