ObjectivesThe primary aim of this cross‐sectional study was to investigate the association between prosthesis design and peri‐implant mucosa dimensions and morphology. The secondary aim was to investigate associations between mucosal dimensions and the presence of mucositis.Materials and MethodsForty‐seven patients with 103 posterior bone level implants underwent clinical and radiographic examination, including cone beam computer tomography and intraoral optical scanning. Three‐dimensional models for each implant and peri‐implant mucosa were constructed. Vertical mucosa height (TH), horizontal mucosa width at implant platform (TW), and 1.5 mm coronal of the platform (TW1.5), as well as mucosal emergence angle (MEA), deep angle (DA), and total contour angle (TA) were measured at six sites for each implant.ResultsThere was a consistent correlation between peri‐implant mucosa width and height (β = 0.217, p < 0.001), with the width consistently surpassing height by a factor of 1.4–2.1. All three angles (MEA, DA, TA) were negatively associated with mucosa height (p < 0.001), while DA was negatively associated with mucosa width (TW1.5) (p < 0.001, β = −0.02, 95% CI: −0.03, −0.01). There was a significant negative association between bleeding on probing (BoP) and mucosa width at platform (OR 0.903, 95% CI: 0.818–0.997, p = 0.043) and 1.5 coronal (OR 0.877, 95% CI: 0.778–0.989, p = 0.033). Implants with less than half sites positive for BoP (0–2/6) had significantly higher mucosa height (OR 3.51, 95% CI: 1.72–7.14, p = 0.001).ConclusionsProsthesis design can influence the dimensions of the peri‐implant mucosa, with wider emergence profile angles associated with reduced peri‐implant mucosa height. In particular, a wider deep angle is associated with reduced mucosa width in posterior sites. Reduced peri‐implant mucosa height and width are associated with more signs of inflammation.Trial RegistrationRegistered in Thai Clinical Trials Registry: http://www.thaiclinicaltrials.org/show/TCTR20220204002.