Model simulations and remote sensing observations show that ocean dynamics at fine scales (1–100 km in space, day–weeks in time) strongly influence the distribution of phytoplankton. However, only few in situ samplings have been performed and most of them in boundary currents which may not be representative of less energetic regions. The PROTEVSMED-SWOT cruise took place in the moderately energetic waters of the western Mediterranean Sea, in the southern region of the Balearic Islands. Taking advantage of near-real time satellite information, a sampling strategy was defined in order to cross a frontal zone separating different water masses. Multi-parametric in situ sensors mounted on the vessel, on a towed fish and on an ocean glider were used to sample at high spatial resolution both physical and biogeochemical variables. A particular attention was put in adapting the sampling route, in order to also estimate the vertical velocities in the frontal area. Such a strategy was successful in sampling quasi-synoptically an oceanic area characterized by the presence of a narrow front with an associated vertical circulation. A multiparametric statistical analysis of the collected data identifies two water masses characterized by different abundances of several phytoplankton cytometric functional groups, as well as different contents in chlorophyll a and O2. Our study shows that the Lagrangian fronts induced by the fine-scale circulation, even if much weaker than the fronts occurring in boundary current systems, maintain a strong structuring effect on phytoplankton community by segregating different taxa at the surface.