Addressing variability in upwelling systems requires combined approaches at different scales. For more than a decade, in vivo/in situ techniques for monitoring phytoplankton are being deployed in different coastal and offshore systems, in the frame of different collaborative national or international projects. As phytoplankton organisms support most marine food webs, mediate main biogeochemical cycles and can also represent a threat to living resources or human health (through the development of Harmful Algal Blooms), it remains crucial to complete discrete sampling and laboratory methods in order to address this compartment at its finest temporal and spatial scale. In that sense, automated in vivo approaches represent a valuable tool, for characterizing phytoplankton communities and exploring their dynamics at high spatial and temporal resolution. In this study, we present some the results of the application of automated in vivo approaches for exploring sub mesoscale features of phytoplankton functional diversity in the Canary Current Upwelling System (CCUS). Two strategies were carried out: the first one, consisted in measurements at different seasons from 2015 to 2018 on a research vessel (“Thalassa” R.V., Ifremer-FOF) and other types of ships (including leisure crafts) in the Southern part of the CCUS (by Sénégal) with a multispectral fluorometer. This approach made it possible to characterize the dynamics of pigmentary/spectral groups, at high spatial resolution, at different stages of the upwelling. Moreover, in the Northern part of the CCUS, the deployment of an automated pulse shape-recording flow cytometer coupled to a multispectral fluorometer was effective during the transit of a research vessel from the Bay of Biscay to the Canary Islands (on its way to the Caribbean Sea) in May 2021 (AMATLANTE-H1 operation on board the “Antéa” R.V., IRD-FOF). It was possible then to describe rapid changes in the spatial distribution of phytoplankton communities characterized by their optical properties related to their functional features. We discuss on the application of these automated optical approaches deployed on both dedicated observations as well as on measurements of opportunity in order to better describing and understanding changing features in upwelling composition and functioning, at multiple scales, in the frame of increasing direct or indirect pressures, from local anthropogenic loads to global change effects.