Breast cancer is a heterogeneous disease and additional biomarkers for individually predicting patient outcomes are needed. Aberrant membrane E-cadherin immunoexpression has been demonstrated in lobular breast cancer. Also, E-cadherin nuclear staining has been reported, associating with prognosis in various tumors. Here, we explore whether membrane or nuclear staining of E-cadherin has the potential to dictate prognosis of patients with lobular breast cancer. We selected a cohort of 285 consecutively diagnosed lobular breast cancer patients and performed immunohistochemistry for E-cadherin (clones 36, EP700Y, and NCH38) and P-cadherin (clone 56C1) in representative formalin-fixed paraffin-embedded blocks. All patients were female, HER2-negative and surgically treated in a single institution. Survival curves were computed by Kaplan-Meier analysis. Hazard ratios and respective 95% confidence intervals were estimated using Cox regression models. Statistical significance was set at p < 0.05. Nuclear staining for E-cadherin clone 36 was frequent (35%), contrarily to other antibodies tested. Negative correlation was found between nuclear and membrane E-cadherin clone 36 immunostaining (r = -0.30, p < 0.001), whereas positive correlation was found between membrane immunoexpression of E-cadherin clone 36 and P-cadherin (r = 0.31, p < 0.001). Patients with any evidence of E-cadherin clone 36 nuclear immunostaining disclosed significantly worse overall survival, disease-specific-survival and disease/progression-free survival (hazard ratio = 2.059, 95% confidence interval 1.313-3.230; hazard ratio = 1.980, 95% confidence interval 1.121-3.495; and hazard ratio = 2.341, 95% confidence interval 1.403-3.905, respectively). Differences in survival were more remarkable when considering nuclear E-cadherin immunoexpression in ≥50% tumor cells. Poorer survival was maintained in multivariable analysis, after adjusting for age, menopausal and PR status, treatment course, vascular invasion, tumor grade and stage. Our results support the use of antibodies against the cytoplasmic domain of E-cadherin, such as clone 36, which may reveal nuclear immunostaining and indicate more aggressive clinical course in patients with lobular breast cancer. We hypothesize that E-cadherin is cleaved and translocated to nucleus functioning as transcription factor.