Stress computed tomography perfusion (Stress-CTP) and computed tomography-derived fractional flow reserve (FFRCT) are functional techniques that can be added to coronary computed tomography angiography (cCTA) to improve the management of patients with suspected coronary artery disease (CAD). This retrospective analysis from the PERFECTION study aims to assess the impact of their availability on the management of patients with suspected CAD scheduled for invasive coronary angiography (ICA) and invasive FFR. The management plan was defined as optimal medical therapy (OMT) or revascularization and was recorded for the following strategies: cCTA alone, cCTA+FFRCT, cCTA+Stress-CTP and cCTA+FFRCT+Stress-CTP. In 291 prospectively enrolled patients, cCTA+FFRCT, cCTA+Stress-CTP and cCTA+FFRCT+Stress-CTP showed a similar rate of reclassification of cCTA findings when FFRCT and Stress-CTP were added to cCTA. cCTA, cCTA+FFRCT, cCTA+Stress-CTP and cCTA+FFRCT+Stress-CTP showed a rate of agreement versus the final therapeutic decision of 63%, 71%, 89%, 84% (cCTA+Stress-CTP and cCTA+FFRCT+Stress-CTP vs cCTA and cCTA+FFRCT: p < 0.01), respectively, and a rate of agreement in terms of the vessels to be revascularized of 57%, 64%, 74%, 71% (cCTA+Stress-CTP and cCTA+FFRCT+Stress-CTP vs cCTA and cCTA+FFRCT: p < 0.01), respectively, with an effective radiation dose (ED) of 2.9 ± 1.3 mSv, 2.9 ± 1.3 mSv, 5.9 ± 2.7 mSv, and 3.1 ± 2.1 mSv. The addition of FFRCT and Stress-CTP improved therapeutic decision-making compared to cCTA alone, and a sequential strategy with cCTA+FFRCT+Stress-CTP represents the best compromise in terms of clinical impact and radiation exposure.