Zooplankton play a key role in the regeneration of nitrogen and phosphorus in the ocean through grazing and metabolism. This study investigates the role of the organic and inorganic nitrogen and phosphorus compounds released by copepods on biogeochemical processes and on the microbial community composition during the OUTPACE cruise (18 February–3 April 2015) at three long duration stations (LD). Two LD stations were located in the Melanesian Archipelago region (MA; LD A and LD B) and one in the South Pacific Gyre (SG; LD C), which represent oligotrophic and ultraoligotrophic regions respectively. At each station, microcosm onboard experiments were performed with locally sampled organisms, comprising a mix of epipelagic copepods fed with their natural food and then incubated along with wild microbial assemblages. In presence of copepods, ammonium and dissolved organic nitrogen showed a significant increase, compared to a control in two situations: in ammonium concentration (increasing rate: 0.29 μmol L−1 h−1 after 4 h of incubation) in LD C and in dissolved organic nitrogen concentration (rate: 2.13 μmol L−1 h−1 after 0.5 h of incubation) in LD A. In addition, during the three experiments, an enhanced remineralization (ammonification and nitrification) was observed when adding copepods compared to the controls. A shift in the composition of active bacterial community was observed for the experiments in LD A and LD B mainly characterized by an increase in Alteromonadales and SAR11, respectively and linked with changes in nutrient concentrations. In the experiment performed in LD C, both groups increased but at different periods of incubation, Alteromonadales between 1 and 2 h after the beginning of the experiment, and SAR 11 at the end of incubation. Finally, our experimental results in near in situ conditions, show that copepods can be a source of organic and inorganic compounds for bacterial communities, which respond to excretion pulses at different scales, depending on the initial environmental conditions and on their community composition. These processes can contribute significantly to nutrient recycling in the epipelagic ecosystem of ultra and oligotrophic oceanic regions.