Calcium phosphates are used in maxillary sinus floor elevation (MSFE) procedures to increase bone height prior to dental implant placement. Whether a collagenous barrier membrane coverage of the lateral window affects bone formation within a bone substitute augmentation is currently an important matter of debate, since its benefit has not been irrefutably proven. Therefore, in this clinical study twelve patients underwent an MSFE procedure with β-tricalcium phosphate (β-TCP). The lateral window was either left uncovered, or covered with a resorbable collagenous barrier membrane. After a 6-months healing period, bone biopsies were retrieved during implant placement. Consecutive 1 mm regions of interest of these biopsies were assessed for bone formation, resorption parameters, as well as bone architecture using histology, histomorphometry and micro-computed tomography. Comparable outcomes between the groups with and without membrane were observed regarding osteoconduction rate, bone and graft volume, osteoclast number and structural parameters of newly formed bone per region of interest. However, osteoid volume in grafted maxillary sinus floors without membrane was significantly higher than with membrane. In conclusion, our results – obtained with a novel method employed using 1 mm regions of interest – demonstrate that the clinical application of a bioresorbable collagenous barrier membrane covering the lateral window, after an MSFE procedure with β-TCP, was not beneficial for bone regeneration and even decreased osteoid production which might lead to diminished bone formation in the long run