Even though most local recurrences after autologous breast reconstruction occur in superficial tissue, they also occur in deep tissue in the reconstructed breast. A 49-year-old woman presented with a bloody discharge from the right nipple. Ultrasonography revealed a hypoechoic area in her right breast, which was diagnosed as ductal carcinoma in situ on histopathology. We performed nipple-sparing mastectomy and immediate reconstruction of the breast with a latissimus dorsi myocutaneous flap. At 6 years postoperatively, the patient presented with a palpable mass. Ultrasonography revealed a solid mass lesion subcutaneously in the right breast. Computed tomography revealed multiple enhanced solid mass lesions in the subcutaneous and deep tissues of the reconstructed breast. The mass in the deep tissue of the reconstructed breast was diagnosed as an invasive micropapillary carcinoma by biopsy. For local recurrence, we performed wide excision of the reconstructed breast. The masses in the subcutaneous and deep tissues of the reconstructed breast were diagnosed as invasive micropapillary carcinoma. Superficial recurrence was first detected by physical examination, and deep recurrence was later detected with further imaging. We present a case of local recurrences that occurred in the deep tissue, in addition to superficial tissue of the reconstructed breast.