Ionospheric models are applied for computing the Total Electron Content (TEC) in ionosphere to reduce its effects on the Global Navigation Satellite System (GNSS)-based Standard Point Positioning (SPP) applications. However, the accuracy of these models is limited due to the simplified model structures and their dependency on the calibration period. In this study, we present a sequential Calibration approach based on the Ensemble Kalman Filter (C-EnKF) to improve TEC estimations. Its advantage, over the frequently implemented state-of-the-art, is that a short period of GNSS network measurements is needed to calibrate model parameters. To demonstrate the results, the International Reference Ionosphere (IRI)-2016 model is used as reference and the Vertical TEC (VTEC) estimates from 53 IGS stations in Europe are applied as observation. The C-EnKF is applied to calibrate four selected model parameters (i.e., IG 12 , U RSI(771), U RSI(1327) and U RSI(1752) related to the ionospheric activity as well as height and density peak-modelling in the F2 layer), which are identified by performing a sensitivity analysis. The calibrated model, called 'C-EnKF-IRI', is localized within Europe and can be used for near-real time TEC estimations and forecasting of the next day (at least). Validation against the dual frequency GNSS measurements of three