Abstract Objectives To validate a novel stepwise strategy in which computed tomography–derived fractional flow reserve (FFR CT ) is restricted to intermediate stenosis on coronary computed tomography angiography (CCTA) and computed tomography myocardial perfusion imaging (CT-MPI) was reserved for vessels with gray zone FFR CT values. Materials and methods This retrospective study included 87 consecutive patients (age, 58 ± 10 years; 70% male) who underwent CCTA, dynamic CT-MPI, interventional coronary angiography (ICA), and fractional flow reserve (FFR) for suspected or known coronary artery disease. FFR CT was computed using a deep learning–based platform. Three stepwise strategies (CCTA + FFR CT + CT-MPI, CCTA + FFR CT , CCTA + CT-MPI) were constructed and their diagnostic performance was evaluated using ICA/FFR as the reference standard. The proportions of vessels requiring further ICA/FFR measurement based on different strategies were noted. Furthermore, the net reclassification index (NRI) was calculated to ascertain the superior model. Results The CCTA + FFR CT + CT-MPI strategy yielded the lowest proportion of vessels requiring additional ICA/FFR measurement when compared to the CCTA + FFR CT and CCTA + CT-MPI strategies (12%, 22%, and 24%). The CCTA + FFR CT + CT-MPI strategy exhibited the highest accuracy for ruling-out (91%, 84%, and 85%) and ruling-in (90%, 85%, and 85%) functionally significant lesions. All strategies exhibited comparable sensitivity for ruling-out functionally significant lesions and specificity for ruling-in functionally significant lesions ( p > 0.05). The NRI indicated that the CCTA + FFR CT + CT-MPI strategy outperformed the CCTA + FFR CT strategy (NRI = 0.238, p < 0.001) and the CCTA + CT-MPI strategy (NRI = 0.233%, p < 0.001). Conclusions The CCTA + FFR CT + CT-MPI stepwise strategy was superior to the CCTA + FFR CT strategy and CCTA+ CT-MPI strategy by minimizing unnecessary invasive diagnostic catheterization without compromising the agreement rate with ICA/FFR. Clinical relevance statement Our novel stepwise strategy facilitates greater confidence and accuracy when clinicians need to decide on interventional coronary angiography referral or deferral, reducing the burden of invasive investigations on patients. Key Points • A stepwise CCTA + FFR CT + CT-MPI strategy holds promise as a viable method to reduce the need for invasive diagnostic catheterization, while maintaining a high level of agreement with ICA/FFR. • The CCTA + FFR CT + CT-MPI strategy performed better than the CCTA + FFR CT and CCTA + CT-MPI strategies. • A stepwise CCTA + FFR CT + CT-MPI strategy allows to minimize unnecessary invasive diagnostic catheterization and helps clinicians to referral or deferral for ICA/FFR with more confidence.