Fluorescence is a practical method implemented in the BioGeoChemical-Argo (BGC-Argo) network for estimating the chlorophyll a concentration (Chla), a widely used proxy of phytoplankton biomass. Despite a strong correlation between the Chla and fluorescence signal on restricted spatial and temporal scales, large regional variations with a clear latitudinal gradient in the Chla-to-fluorescence ratio, referred to as “slope factor”, have been observed in the global ocean. This indicates the potential influence of phytoplankton community composition, resulting from the combined effects of phytoplankton absorption and quantum yield of fluorescence. As phytoplankton communities play a key role in global biogeochemical cycles, it is critical to understand their variability to accurately determine Chla. In order to examine the role of phytoplankton community composition on the fluorescence signal, we used a global concurrent dataset of Chla estimated from BGC-Argo float fluorescence measurements and High-Performance Liquid Chromatography determinations, as well as phytoplankton absorption measurements. The community composition of phytoplankton shows a strong influence on absorption, with smaller cells characterized by reduced package effect and high absorption by accessory pigments in the blue spectral region. The quantum yield of fluorescence presents a clear trend with lower values in oligotrophic areas than in high latitude regions. In oligotrophic regions, picophytoplankton exhibit low values of the fluorescence quantum yield, which we attribute to the non-photosynthetic pigment zeaxanthin. The present work, showing that the slope factor is significantly correlated to the size structure of phytoplankton communities, is a first step towards a better estimation of Chla from BGC-Argo floats. Different methods have been proposed for assessing community size structure from BGC-Argo floats and thus could be used to better constrain the calibration of fluorescence in Chla.