Introduction: Intraoperative radiation therapy (IORT) is an alternative to external beam radiation therapy (EBRT) after lumpectomy, in which radiation is delivered before the final margin analysis. Practices vary regarding excision of close or positive margins pre- and post-IORT. Materials and methods: In a retrospective cohort of women with hormone receptor-positive, clinically node-negative breast cancer undergoing lumpectomy with IORT and selective EBRT at our institution from 2011 to 2015, we compared the impact of pre- and post-IORT margin excisions on in-breast tumor recurrence. Additional pre-IORT margins were taken at surgical team discretion. Re-excisions post-IORT were performed for positive/close margins. We describe rate of invasive or in situ malignancy in additional pre-IORT and post-IORT re-excised specimens and compare IBTR using Chi-squared tests. Results: There were 195 cases in 193 women (2 bilateral breast cancer). Pre-IORT, ≥1 additional margin was obtained in 139 (71%). The final margin on the initial lumpectomy was positive in 13 (9%) and ≤2 mm in 72 (52%). Additional pre-IORT margins contained in situ/invasive cancer in 16 (12%). Thirty-one patients (16%) underwent post-IORT re-excision and nine (29%) contained invasive/in situ malignancy. Twenty-three (12%) received EBRT. In 45.6-month mean follow-up, 13 had IBTR (7%) with no difference by additional pre-IORT margin excision (5 vs. 11%, p = 0.150), post-IORT margin re-excision (10 vs. 6%, p = 0.464), or EBRT (0 vs. 8%, p = 0.172). Adjuvant endocrine therapy was associated with lower IBTR (4 vs. 17%, p = 0.003). Conclusions: Taking additional pre-IORT margins and re-excising close/positive margins post-IORT improved margin clearance rates but had an unclear effect on IBTR. Adjuvant endocrine therapy significantly reduced IBTR.