A new approach for processing the remote sensing chlorophyll-α (Chl-α) before assimilating into an ecosystem model is applied in two contrasting, regarding productivity and nutrients availability, Mediterranean sites: the DYFAMED and POSEIDON E1-M3A fixed point open ocean observatories. The new approach derives optically weighted depth-distributed Chl-α profiles from satellite data based on the model simulated Chl-α vertical distribution and light attenuation coefficient. We use the 1D version of the operational ecological 3D POSEIDON model, based on the European Regional Seas Ecosystem Model (ERSEM). The required hydrodynamic properties are obtained (off-line) from the POSEIDON operational 3D hydrodynamic Mediterranean basin scale model. The data assimilation scheme is the singular evolutive interpolated Kalman (SEIK) filter, the ensemble variant of the singular evolutive extended Kalman (SEEK) filter. The performance of the proposed assimilation approach was evaluated against the Chl-α satellite data and the seasonal averages of available in situ data for nitrate, phosphate and Chl-α. An improvement of the model simulated near-surface and subsurface maximum Chl-α concentrations is obtained, especially at the DYFAMED site. Model nitrate is improved with assimilation, particularly with the new approach assimilating depth-distributed Chl-α, while model phosphate is slightly worse after assimilation. Additional sensitivity experiments were performed, showing a better performance of the new approach under different scenarios of model Chl-α deviation from pseudo-observations of surface Chl-α.