This review aims at discussing the molecular details of the folding mechanisms of conjugated proteins using computational tools. Almost all studies of protein folding focus on individual proteins and do not consider how interactions with posttranslational modifications and between domains might affect folding. However, different chemical conjugations may introduce a variety of effects on the protein biophysics. These effects depend both on the chemical characteristics of the protein substrate as well as on the chemical and physical properties of the attachment. We review the folding of various types of conjugated proteins, glycoproteins, proteins with tails, ubiquitinated proteins, and multidomain proteins, to explore the underlying biophysical principles of these complex folding processes and in particular to quantify the cross-talk between the protein and its conjugated polymer.