In this chapter, we provide an overview of the different modes of modifications that are employed in covalent organic framework (COF) chemistry: (i) in situ modification, (ii) pre-synthetic modification, and (iii) post-synthetic modification. In addition to covalent modification of the framework backbone and metalation at pre-installed binding sites, the trapping of functional guests in the pores or within the extended crystals of COFs is discussed. The applicability and intrinsic limitations of the various approaches of framework modification are evaluated.