Background: Free-handed, flaplessly placed mini dental implants (MDIs) are a valuable, more affordable and minimally invasive treatment to support overdentures in fully edentulous jaws, especially for medically compromised patients. However, critical 3D radiographic evaluation is lacking. This multicenter prospective case series assessed clinical outcome and carried out 3D- cone-beam computerized tomography (CBCT) analysis of free-handed flaplessly placed one-piece maxillary MDIs by an experienced maxillofacial surgeon. Methods: Thirty-one patients suffering from an ill-fitting maxillary denture relating to compromised bone volume (as confirmed on CBCT), with a dentate mandible, were selected. They received 5–6 MDIs free-hand flaplessly placed and mentally guided with preoperative CBCT. Final connection and attachment activation took place six months later. After two years each implant was individually assessed with CBCT for perforations on eight sites. Implant survival, prosthetic failure, clinical stability and sinus/nasal complaints were registered after three years. Results: 32/185 (17.3%) MDIs failed during the provisional loading with non-activated attachments; 17 replacements in 10 patients were performed. Of the 170 actively loaded 170 MDIs, 82.3% survived and 27/31 prostheses (87%) were fully functional. In total 98/170 MDIs showed no perforation. Based on 1360 CBCT observations, 231 perforations (16.9%) were registered. Of most perforations 37 (25%) were observed at the apical tip and 37 were positioned (21%) into the sinus/nasal cavity, although without clinical complaints. Conclusions: Given the compromised population, the minimally invasive procedure and the low treatment cost involved, a failure rate of 17% is substantial, however clinically acceptable given the critical bone condition. However, even in experienced surgical hands, freehanded and flapless placement yield a high risk for implant perforation, although this did not necessarily lead to complications.