Ti$_3$C$_2$T$_x$ is a leading compound within the MXenes family and can find host in widespread applications. It is synthesized by selectively etching layers from the Ti$_3$AlC$_2$ precursor, and this process typically introduces surface terminations, T$_x$, such as $-$OH, $=$O, or $-$F. However, the aggressive chemical conditions required for its preparation, as well as exposure to air, humidity, and heat, can lead to impurity phases that potentially compromise its desirable properties. We reveal a two-step oxidation process during heat treatment, where initial oxidation occurs between layers without altering the integrity of the Ti$_3$C$_2$ layered structure, followed by the formation of anatase TiO$_2$ at elevated temperatures. The process was carefully monitored using \emph{in situ} Raman spectroscopy and \emph{in situ} microwave conductivity measurements, employed to Ti$_3$C$_2$T$_x$ prepared using various etching techniques involving concentrated HF, LiF + HCl, and HF + HCl mixtures. The oxidation process is heavily influenced by the synthesis route and surface chemistry of Ti$_3$C$_2$T$_x$, with fluoride and oxyfluoride groups playing a pivotal role in stabilizing the anatase phase. The absence of these groups, in contrast, can lead to the formation of rutile TiO$_2$.