Background: Trastuzumab deruxtecan (T-DXd) was recently approved to treat unresectable/metastatic HER2-low breast cancer. However, patients whose primary tumor is HER2-0 but recurrent/metastatic lesion is HER2-low will lose therapeutic opportunities for T-DXd if a rebiopsy is not performed. In this study, with the largest sample size to date, we aimed to investigate the prevalence of HER2 status conversion. Moreover, it remains debated whether HER2-0 and HER2-low tumors have different prognoses, probably because previous studies did not assess HER2 status entirely based on recurrent/metastatic lesions. Our study aimed to fill this gap. Methods: We included 1299 patients with available HER2 status on both primary tumors and recurrent/metastatic lesions at Fudan University Shanghai Cancer Center and West China Hospital. Results: A total of 370 (28.5%) patients experienced HER2 status conversion throughout disease recurrence. 144 (31.7%) HER2-0 tumors converted to HER2-low. Inter-metastases heterogeneity of HER2 status was also observed. Compared to HER2-low tumors, HER2-0 tumors showed a higher TP53 mutation rate in the ER-positive subgroup, and a lower PIK3CA mutation rate in the ER-negative subgroup. Patients with tumors converting from HER2-0 to HER2-low had a longer overall survival (HR = 0.59, adjusted P = 0.033) than those with consistent HER2-0 status in the ER-negative subgroup. By combining four risk factors (ER status, Ki67 index, biopsy site, and disease-free interval), we established the first prediction tool to estimate the probability of HER2 status conversion from HER2-0 to HER2-low/positive. Conclusions: HER2 status was unstable during the disease course. Our prediction tool could help to screen out patients with a high probability of HER2 status conversion. Our results support that HER2-0 and HER2-low recurrent/metastatic tumors have different genomic features and prognoses.