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 a few in situ-based studies at fine scales have been performed, and most of them concern western 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 (WMS), in the region south of the Balearic Islands. Taking advantage of near-real-time satellite information, we defined a sampling strategy in order to cross a frontal zone separating different water masses. Multi-parametric in situ sensors mounted on the research vessel, on a towed vehicle and on an ocean glider were used to sample physical and biogeochemical variables at a high spatial resolution. Particular attention was given to adapting the sampling route in order to estimate the vertical velocities in the frontal area also. This 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 concentrations of chlorophyll a and O2. Here, we focus on moderately energetic fronts induced by fine-scale circulation. Moreover, we explore physical–biological coupling in an oligotrophic region. Our results show that the fronts induced by the fine-scale circulation, even if weaker than the fronts occurring in energetic and nutrient-rich boundary current systems, maintain nevertheless a strong structuring effect on the phytoplankton community by segregating different groups at the surface. Since oligotrophic and moderately energetic regions are representative of a very large part of the world ocean, our results may have global significance when extrapolated.