Three different novel chitosan derivatives for medical or biotechnological applications have been successfully obtained by chemical modification of reactive amino and hydroxyl groups in chitosan chain. The modification has led to incorporation of different amount (one to three) of long-distanced amino and imine groups into each repeating unit. These highly functionalized chitosan derivatives were used as a matrix for magnetite nanoparticles. The thermal stability of all obtained chitosan materials has been determined using thermogravimetric analysis in oxidative and inert atmosphere. Chitosan containing two side substituents behaves differently from the other two, which is caused by the significant water uptake. Magnetite causes decrease in thermal stability of studied chitosan derivatives. The highest stability is observed for the nanocomposite obtained from chitosan with three side groups. The changes in the structure of the magnetite core have been observed above 600 °C in nitrogen. Due to the different competitive reactions occurring in the modified chitosan, the proposed mechanism of thermal degradation is very complex.