Abstract Background Fibroepithelial lesions (FEL) are a heterogeneous group of biphasic tumours that include fibroadenomas (FA) and the rare entity of benign phyllodes tumors (PT) as well as cases where distinction between these two entities is not possible. The histologic distinction between benign PT and cellular FA is still a diagnostic challenge, especially in core-needle biopsy (CNB) or vacuum-assisted biopsy (VAB). Guidelines are not clearly established regarding the management of FEL in CNB or VAB. In this study, we addressed the frequency of B3 FEL diagnosed in CNB or VAB and compared the final histopathological findings in the excision specimens to evaluate up- or downgrading. Methods We identified 117 female patients with the preoperative diagnosis of FEL (B3), PT, or FEL in combination of pure epithelial B3 lesions in CNB or VAB. Clinico-pathological information as well as data on subsequent surgical excision were available for all patients. Results PT was diagnosed in 9 (14.8%) and FEL (B3) in 52 (85.2%) cases. Additionally, 56 patients with FA in combination with an additional B3 lesion were identified. Most FEL (B3)/PT initial diagnoses were made in CNB (55.6% of PT; 84.6% of FEL). After the initial biopsy, 7 of 9 (77.8%) patients with initial diagnosis of benign or borderline PT in CNB/VAB and 40 of 52 (77.0%) patients with initial diagnosis of FEL (B3) in CNB/VAB underwent open excision (OE). 4 of 9 cases (44.4%) initially diagnosed as PT were verified, whereas 2 of 9 (22.2%) were downgraded to FA. 20 of 52 cases (38.5%) initially diagnosed as FEL (B3) were downgraded to FA, whereas 11 of 52 cases (21.2%) were diagnosed as benign or borderline PT. One FEL (B3) case was upgraded to malignant PT. Conclusion Most PT and FEL (B3) diagnoses on CNB/VAB underwent surgical removal. In the final pathological findings of cases classified primarily as FEL (B3), the majority were downgraded to FA, one quarter were upgraded to PT, and a small subset remained as combined FA/PT. In clinical daily practice, we recommend individualized decision-making considering different options (clinical follow-up or removal of the lesion depending on the whole context) in a multidisciplinary preoperative conference.