(1) Background: This work aimed to conduct the first comparative study providing long-term data about patient reported outcome measures as well as donor-site scar assessment and aesthetic evaluation of the reconstructed breasts in patients with DIEP versus PAP flap breast reconstruction. (2) Methods: This prospective, single-center, matched cohort study included a total of 36 patients after DIEP and PAP flap breast reconstruction. Evaluation was done using the Breast-Q and POSAS questionnaire as well as the Breast Aesthetic Scale for cosmetic analysis by four plastic surgeons. (3) Results: Post-operative Breast-Q evaluation revealed no significant differences between both patient groups for the categories physical well-being donor-site, physical well-being breast and satisfaction with the breast. Scar evaluation of the donor-site region showed equivalent results for the thigh and the abdomen concerning the overall opinion of patients and observers. There was no significant difference between both methods of reconstruction for all aspects of breast aesthetics. (4) Conclusions: Similar results of donor-site morbidity, scar quality and aesthetic outcome of the breast in both the DIEP and PAP patient group have been demonstrated. Hence, in cases suitable for both types of reconstruction, the decision can be based on factors such as patients’ lifestyle, leisure activities and preferences.