This study aims to assess the treatment outcomes (functional and subjective) of full-arch fixed hybrid rehabilitations made of PEEK (poly-ether-ether-ketone) with milled crowns of nano-filled composite (NFC) supported on four to six implants. In this randomized clinical trial, 34 edentate patients in the upper and/or the lower jaws were treated with the fixed hybrid dentures. In 16 patients (47.1% of the sample), the implants were loaded immediately (IL) by means of a provisional fixed rehabilitation made of PMMA (polymethylmethacrylate) screwed on Multi-Unit (MU) abutments connected after emplacement of the implant; however, in the counterparts (n = 18) these MU abutments were covered by healing caps and were left unloaded during two months (conventional loading protocol—CL), when all patients received a fixed hybrid PEEK-NFC rehabilitation on the upper and/or the lower jaw. Treatment outcomes were assessed 12 months after prostheses delivery. Functional outcomes were calculated according to masticatory performance, estimated by mixing ability tests of two colored chewing gums after ten chewing strokes, by the occlusal force/area recorded by pressure-sensitive sheets, and by electromyography of masseters and temporal muscles at maximum biteforce. The subjective outcomes of the treatment were assessed using both the oral satisfaction scale (visual analog scale) and the Spanish version of the Oral Health Impact Profile (OHIP-20). The findings of the present study showed that treatment with fixed PEEK-NFC hybrid prostheses significantly improved the masticatory performance, bite force, occlusal pattern, quality of life, and satisfaction, with the IL group being those with significantly higher occlusal bite forces and greater satisfaction in comparison with CL group. It should be concluded that PEEK-NFC hybrid prostheses can improve several patient-centered outcomes and that loading protocol significantly affects the patient’s self-rated satisfaction.