© 2018 Author(s). Laser Interferometer Space Antenna (LISA) Pathfinder is a mission to test the technology enabling gravitational wave detection in space and to demonstrate that sub-femto-g free fall levels are possible. To do so, the distance between two free falling test masses is measured to unprecedented sensitivity by means of laser interferometry. Temperature fluctuations are one of the noise sources limiting the free fall accuracy and the interferometer performance and need to be known at the ∼10 μK Hz-1/2 level in the sub-millihertz frequency range in order to validate the noise models for the future space-based gravitational wave detector LISA. The temperature measurement subsystem on LISA Pathfinder is in charge of monitoring the thermal environment at key locations with noise levels of 7.5 μK Hz-1/2 at the sub-millihertz. However, its performance worsens by one to two orders of magnitude when slowly changing temperatures are measured due to errors introduced by analog-to-digital converter non-linearities. In this paper, we present a method to reduce this effect by data post-processing. The method is applied to experimental data available from on-ground validation tests to demonstrate its performance and the potential benefit for in-flight data. The analog-to-digital converter effects are reduced by a factor between three and six in the frequencies where the errors play an important role. An average 2.7 fold noise reduction is demonstrated in the 0.3 mHz-2 mHz band.