In recent years, the Global Navigation Satellite Systems (GNSS) have been intensively modernized, resulting in the introduction of new carrier frequencies for GPS and GLONASS and the development of new satellite systems such as Galileo and BeiDou (BDS). For this reason, the absolute field antenna calibrations performed so far for the two legacy carrier frequencies, the GPS and GLONASS, seem to be insufficient. Hence, all antennas will require a re-calibration of their phase center variations for the new signals to ensure the highest measurement accuracy. Currently, two absolute calibration methods are used to calibrate GNSS antennas: field calibration using a robot and calibration in an anechoic chamber. Unfortunately, differences in these methodologies also result in a disparity in the obtained antenna phase center corrections (PCC). Therefore, we analyze the differences between individual PCC obtained with these two methods, specifically for the Leica AR-25 antenna model (LEIAR25). In addition, the influence of PCC differences on the GNSS-derived position time series for 19 EUREF Permanent GNSS Network (EPN) stations was also assessed. The results show that the calibration method has a noticeable impact on PCC models. PCC differences determined for the ionosphere-free combination may reach up over 20 mm and can be transferred to the position domain. Further tests concerning the positioning accuracy showed that for horizontal coordinates differences between solutions were mostly below 1 mm, exceeding 2 mm only at two stations for the GLONASS solution. However, the height component differences exceeded 5 mm for four, six and six stations out of 19 for the GPS, GLONASS and Galileo solutions, respectively. These differences are strongly dependent on large L2 calibration differences.