Background <p>Pupillary capture can cause complications after intrascleral intraocular lens (IOL) fixation; however, no method has been established to definitively prevent pupillary capture. Therefore, we aimed to examine the differences in the incidence of pupillary capture in patients who underwent intrascleral IOL fixation and had intraoperative lens capsule preservation or lens capsule loss.</p> Methods <p>This single-center, retrospective study, conducted at a University Hospital, included 83 eyes from 83 patients. The eyes were allocated to the capsule and no-capsule groups based on the presence or absence of capsule, respectively. Patient demographics, causative diseases, incidence of pupillary capture at 1 year postoperatively, anterior chamber depths (ACDs), IOL tilts, and decentrations of the two groups were analyzed and compared.</p> Results <p>The capsule and no-capsule groups comprised 26 and 57 eyes, respectively. The indications for intrascleral IOL fixation were: IOL dislocation in 6 (23.1%) and 41 (71.9%), artificial aphakia in 4 (15.4%) and 2 (3.5%), conversion during cataract surgery due to complications (zonular dialysis or posterior capsule rupture) in 14 (53.9%) and 3 (5.3%), lens dislocation in 0 and 11 (19.3%), and IOL opacification in 2 (7.7%) and 0 eyes in the capsule and no-capsule groups, respectively (<i>P</i> &lt; 0.05). The postoperative outcomes including ACD, magnitude of tilt, or decentration of the fixed IOL did not differ between the two groups (<i>P</i> &gt; 0.05). Pupillary capture was observed in eight eyes, all in the no-capsule group (<i>P</i> &lt; 0.05).</p> Conclusions <p>When performing intrascleral fixation in cases where the lens capsule remains, preserving the capsule and fixing the IOL under the capsule may prevent postoperative pupillary capture.</p>