A high priority goal for past, present and future missions to Mars is the search for evidence of past or present life. Some of the most information-rich signals are those represented by organic biomarkers. Thermal extraction has historically been the most popular in situ analysis technique employed on Mars owing to its elegance and ability to liberate both small compounds and large macromolecular networks. The geological record of Mars contains a variety of minerals, some of which can interact with organic matter when subjected to thermal extraction. Here we discuss the organic records that may be associated with these mineral hosts and the problems encountered when mineral-organic mixtures are analysed by thermal-based methods. We also suggest potential mitigations for future experiments of a similar nature and note that these mitigating steps can be applied not only in situ on Mars but also after samples are returned to Earth as part of Mars Sample Return where more resources and time for sample preparation are available.