Background Cerebral microbleeds (CMBs) are increasingly recognized as “covert” brain lesions indicating increased risk of future neurological events. However, data on CMBs in patients undergoing catheter‐based structural heart interventions are scarce. Therefore, we assessed occurrence and predictors of new CMBs in patients undergoing catheter‐based left atrial appendage closure and percutaneous mitral valve repair using the MitraClip System. Methods and Results We conducted an exploratory analysis using data derived from 2 prospective, observational studies. Eligible patients underwent cerebral magnetic resonance imaging (3 Tesla) examinations and cognitive tests (using the Montreal Cognitive Assessment) before and after catheter‐based left atrial appendage closure and percutaneous mitral valve repair. Forty‐seven patients (53% men; median age, 77 years) were included. New CMBs occurred in 17 of 47 patients (36%) following catheter‐based structural heart interventions. Occurrences of new CMBs did not differ significantly between patients undergoing catheter‐based left atrial appendage closure and percutaneous mitral valve repair (7/25 versus 10/22; P =0.348). In univariable analysis, longer procedure time was significantly associated with new CMBs. Adjustment for heparin attenuated this association (adjusted odds ratio [per 30 minutes]: 1.77 [95% CI, 0.92–3.83]; P =0.090). Conclusions New CMBs occur in approximately one‐third of patients after catheter‐based left atrial appendage closure and percutaneous mitral valve repair using the MitraClip System. Our data suggest that longer duration of the procedure may be a risk factor for new CMBs. Future studies in larger populations are needed to further investigate their clinical relevance. Clinical Trial Registration German Clinical Trials Register: DRKS00010300 ( https://drks.de/search/en/trial/DRKS00010300 ); ClinicalTrials.gov : NCT03104556 ( https://clinicaltrials.gov/ct2/show/NCT03104556?term=NCT03104556&draw=2&rank=1 ).