The presence or absence of prawn shell impacts the cooked muscle quality. Here, we evaluated the effect of different cooking temperatures and times during water bath treatment on the quality attributes of peeled and unpeeled prawns. Several factors, including heat penetration, moisture content, color distribution, microstructure, and texture changes were tested. Thermal protein denaturation was assessed to clarify differences in quality attributes between both samples. Heat penetration was slightly slower in unpeeled prawns compared to peeled prawns, which correlated with the lower denaturation rate for each protein (myosin, sarcoplasmic-collagen, and actin). The tissue connection between the shell and muscle protects the prawn meat from shrinkage, resulting in reduced water release. Maximum stress at 50, 65, and 75 C was significantly higher in unpeeled prawns than in peeled prawns. However, the absence of shell resulted in a denser microstructure and slightly higher color profile in peeled prawns. These findings may be applied for the thermal processing of prawns.