Objectives MR-guided daily-adaptive radiotherapy is improving the accuracy in the planning and delivery phases of the treatment. Rectal hydrogel-spacer may help in mitigating organ motion, but few data are currently available. Methods We aimed to assess any potential impact of the device on seminal vesicles motion by measuring translational and rotational shifts between the pre- and post-treatment MRI scans of a total of 50 fractions in the first 10 patients who underwent MR-guided prostate SBRT (35 Gy/5 fx). Of them, five patients received the hydrogel-spacer. The comparative analysis was performed using the Mann–Whitney U-test Results Median rotational shifts were: in anteroposterior 0° (range, 0.097°/0.112°; SD = 0.05°) vs 0° (−0.162/0.04°; SD = 0.07°) in the no-spacer subgroup (p = 0.36); lateral shifts were 0° (−0.1°/0.54°; SD = 0.28°) vs −0.85° in the no-spacer cohort (−1.56°/0.124°; SD = 0.054°; p = 0.22). Cranio-caudal shifts were 0° (−0.121°/0.029°; SD = 0.06°) in the spacer-cohort vs 0° (−0.066°/0.087°; SD = 0.69°; p = 0.53). Median translational shifts were: in anteroposterior 0.9 mm (−0.014 mm/0.031 mm; SD = 0.036 mm) in the spacer-group vs 0.030 mm (−0.14 mm/0.03 mm; SD = 0.032 mm; p = 0.8); latero-lateral shifts were −0.042 mm (−0.047 mm/0.07 mm; SD = 0.054 mm), vs −0.023 mm (−0.027 mm/−0.01 mm; SD = 0.023 mm) in the no-spacer group (p = 0.94). In cranio-caudal, statistically significant shifts were reported: 0.082 mm (0.06 mm/0.15 mm; SD = 0.04 mm) vs 0.06 mm (−0.06/0.08 mm; SD = 0.09 mm) in the no-spacer cohort (p = 0.031). Conclusions A favorable impact of the hydrogel-spacer on seminal vesicles motion was observed only in cranio-caudal translational shifts, although being not clinically significant. Further studies are required to fully investigate the potential contribution of this device on vesicles motion. Advances in knowledge MR-guided daily adaptive radiotherapy may represent a game changer for prostate stereotactic body radiotherapy, given the possibility to better visualize soft-tissues anatomy and to daily recalculate the treatment plan based on real-time conditions. The use of devices like rectal ballon or rectal gel spacers has gained interest in the last years for the possibility to better spare the rectum during prostate radiotherapy. This is one of the first experiences exploring the role of rectal spacer on seminal vesicles intrafraction motion during MR-guided SBRT for prostate cancer.