Phytoplankton pigments were determined in the water surface (from 0 to 11 m depth) of a transect from the North Sea to East Greenland Sea and back during RV Polarstern expedition PS131 from 29 Jun to 3 Aug 2022. Water samples were collected from CTD Niskin bottles at five to six different depths from the upper 100 m at CTD stations and from underway sampling. Between 0.4 to 3.5 L of each seawater sample was filtered through Whatman GF/F filters. The sample filters were then shock‐frozen in liquid N2 and kept at −80 °C until analysis. High Pressure Liquid Chromatography (HPLC) was performed to quantify various phytoplankton pigments (see Table 1 in Taylor et al. 2011) following the method of Barlow et al. (1997) that was adjusted to our temperature‐controlled instruments as detailed in Alvarez et al. (2022). Data were used to analyse the Fram Strait phytoplankton community composition dynamics in Bracher et al. (submitted to DSR-II).