The room temperature synthesis of two Co-based hybrid layered hydroxides containing the same organic ligand (suberate [Sub]), one connected through purely electrostatic interactions (CoAl layered double hydroxide [LDH]), and the other covalently functionalized (α-CoII simonkolleite phase) has been carried out. The magnetic properties exhibit an acute difference in the magnetization temperatures (from ≈10 K for the CoAl-LDH to ≈55 K for the α-CoII). Moreover, the role of the covalent functionalization in the thermal stability and the decomposition has been investigated by a forefront characterization tool consisting of thermogravimetric analysis coupled with gas chromatography and mass spectrometry (TG-GC-MS). The LDH exhibits a higher thermal stability of ≈50 ºC with broad mass loss steps, whereas the water molecules interact stronger with the α-CoII(Sub) hybrid, suggesting a higher confinement in the interlayer space. Interestingly, at higher temperatures (>400 ºC), the α-CoII(Sub) gives rise to the selective formation of cycloheptanone, in contrast to the LDH phase leading to different carbonyl containing compounds. These findings offer new fundamental insights into the thermal behavior of hybrid materials based on layered hydroxides, highlighting the important role of covalent functionalization in its properties.