Methods and systems for precise temperature and timebase PPM error estimation using multiple timebases may comprise in an electronic device comprising a plurality of timebases and measuring a temperature corresponding to the timebases. Frequencies of the timebases at the measured temperature may be compared to determine differential error functions for the timebases. A fine reading of the temperature corresponding to the timebases may be generated based, at least in part, on the measured temperature and the determined differential error functions for the timebases. The timebases may be calibrated utilizing the generated fine reading of the temperature. The timebases may comprise different order temperature dependencies. Models of temperature dependencies of each of the timebases based may be updated, at least in part, on the fine reading of the temperature. A global navigation satellite system (GNSS) clock signal may be periodically utilized to improve the accuracy of the calibration of the timebases.