Filaments and fronts play a crucial role for a net offshore and downward nutrient transport in Eastern Boundary Upwelling Systems (EBUSs) and thereby reduce regional primary production. Most studies on this topic are based on either observations or model simulations, but only seldom are both approaches are combined quantitatively to assess the importance of filaments for primary production and nutrient transport. Here we combine targeted interdisciplinary shipboard observations of a cold filament off Peru with submesoscale-permitting (1/45∘) coupled physical (Coastal and Regional Ocean Community model, CROCO) and biogeochemical (Pelagic Interaction Scheme for Carbon and Ecosystem Studies, PISCES) model simulations to (i) evaluate the model simulations in detail, including the timescales of biogeochemical modification of the newly upwelled water, and (ii) quantify the net effect of submesoscale fronts and filaments on primary production in the Peruvian upwelling system. The observed filament contains relatively cold, fresh, and nutrient-rich waters originating in the coastal upwelling. Enhanced nitrate concentrations and offshore velocities of up to 0.5 m s−1 within the filament suggest an offshore transport of nutrients. Surface chlorophyll in the filament is a factor of 4 lower than at the upwelling front, while surface primary production is a factor of 2 higher. The simulation exhibits filaments that are similar in horizontal and vertical scale compared to the observed filament. Nitrate concentrations and primary production within filaments in the model are comparable to observations as well, justifying further analysis of nitrate uptake and subduction using the model. Virtual Lagrangian floats were released in the subsurface waters along the shelf and biogeochemical variables tracked along the trajectories of floats upwelled near the coast. In the submesoscale-permitting (1/45∘) simulation, 43 % of upwelled floats and 40 % of upwelled nitrate are subducted within 20 d after upwelling, which corresponds to an increase in nitrate subduction compared to a mesoscale-resolving (1/9∘) simulation by 14 %. Taking model biases into account, we give a best estimate for subduction of upwelled nitrate off Peru between 30 %– 40 %. Our results suggest that submesoscale processes further reduce primary production by amplifying the downward and offshore export of nutrients found in previous mesoscale studies, which are thus likely to underestimate the reduction in primary production due to eddy fluxes. Moreover, this downward and offshore transport could also enhance the export of fresh organic matter below the euphotic zone and thereby potentially stimulate microbial activity in regions of the upper offshore oxygen minimum zone.