Chlorophyll-a, the most important photosynthetic pigment of marine phytoplankton, is one of the basic marine biogeochemical variables. Chlorophyll-a concentration can be measured by applying high-performance liquid chromatography (HPLC) techniques to filtered water samples, which is greatly limited by time and number of samples. The inherent optical properties (IOPs) of seawater are proved to have good linkage to biogeochemical variables. With the emergency of in situ optical sensors, high spatial and temporal resolution measurements of bio-optical properties are achievable, making it possible to understand ocean biogeochemical processes on a broader scale. However, data quality control of the optical sensors remains challenging because of biofouling and the instrumental instability. In this study, we established a ship-based flow-through system of Absorption Attenuation Spectra Meter (AC-s) and conducted continuous underway measurements of hyperspectral IOPs during the PS93.2 expedition to the Fram Strait. The system collected periodical measurements of total and 0.2 μm cartridge filtered absorption and attenuation, allowing for the calculation of particulate absorption and attenuation by differencing the corresponding IOPs of the total and filtered seawater. The continuous particulate absorption coefficients were then averaged to 1-min intervals, compared and corrected with discrete filter-pad measurements. The near-surface phytoplankton Chlorophyll-a concentrations were finally retrieved from the quality controlled hyperspectral particulate absorption based on empirical orthogonal functions in the Fram Strait.