Thermal degradation of modified pectin samples with varying molecular structure during storage was recently studied at 60 °C and 80% relative humidity (rh) for 28 days. Demethoxylation and depolymerisation were identified as main degradation reactions. The present paper aims on improving the understanding of the different depolymerisation reactions and their interplay with demethoxylation during storage. Therefore, thermal degradaton of acidic and alkaline demethoxylated pectins was studied at a further reduced rh of 40%. The alterations were examined in detail via molecular parameters and were reflected by Differential scanning calorimetry and attenuated total reflectance Fourier-transformation infrared spectroscopy. The impact of thermal degradation on pectin particle structure was studied via particle surface area and microscopy.At low relative humidity (rh) demethoxylation and depolymerisation were reduced, and the formation of brown reaction products, resulting from further decomposition of intermediate uronides and neutral sugars, was restricted. By comparing thermal degradation at different humidity, eliminative decarboxylation was identified as the main depolymerisation reaction.Reduction of rh affected also the alteration of pectin material properties, particle surface reduction was less pronounced. Molecular alterations were stronger in case of acidic demethoxylated samples, and alterations of material properties were higher in case of alkaline demethoxylated samples.