Background People with intellectual disabilities often have a multitude of concurrent problems due to the combination of cognitive impairments, psychiatric disorders (particularly anxiety) and related challenging behaviours. Diagnoses in people with intellectual disabilities are complicated. This study evaluates the quality of the diagnoses and treatment plans after using a guideline that was developed to support professionals in their diagnostic tasks. Materials and Methods A comparative multiple case study with an experimental and control condition, applying deductive analyses of diagnoses and treatment plans. Results The analyses revealed that the number of diagnostic statements and planned treatment actions in the experimental group was significantly larger and more differentiated than in the control condition. In the control group, consequential harm and protective factors were hardly mentioned in diagnoses and treatment plans. Conclusions Working with the ‘Diagnostic Guideline for Anxiety and CB’ leads to improved diagnoses and treatment plans compared with care as usual.