Abstract Background Guideline adherence with respect to exercise-based cardiac rehabilitation (CR) is hampered by a large variety of complex guidelines and position statements, and the fact that these documents are not specifically designed for healthcare professionals prescribing exercise-based CR programs. This study aimed to develop clinical algorithms that can be used in clinical practice for prescription and evaluation of exercise-based CR in patients with coronary artery disease (CAD) and chronic heart failure (CHF). Methods The clinical algorithms were developed using a systematic approach containing four steps. First, all recent Dutch and European cardiac rehabilitation guidelines and position statements were reviewed and prioritised. Second, training goals requiring a differentiated training approach were selected. Third, documents were reviewed on variables to set training intensity, modalities, volume and intensity and evaluation instruments. Finally, the algorithms were constructed. Results Three Dutch guidelines and three European position statements were reviewed. Based on these documents, five training goals were selected and subsequently five algorithms for CAD patients and five for CHF patients were developed. Conclusions This study presents evidence-based clinical algorithms for exercise-based CR in patients with CAD and CHF according to their training goals. These algorithms may serve to improve guideline adherence and the effectiveness of exercise-based CR.