Mitochondrial dysfunction is common in cancer, and the mitochondrial electron chain is often affected during carcinogenesis. This study provides a comprehensive analysis of the ATP5F1 gene family to explore ATP5F1A, B, C, D, and E genes for their expression and prognostic values in breast cancer. Gene expression data were obtained from GEO dataset and TCGA, enabling the assessment of differential expression, survival correlations, and tumor grade-specific expression. Protein expression data was obtained from the Human Protein Atlas, mutation frequencies were retrieved from cBioPortal, and functional enrichment was performed using Enrich. Correlations with immune cell infiltration were also evaluated using TIMER. Notably, our investigation revealed that ATP5F1C, ATP5F1D, and ATP5F1E were highly upregulated, while ATP5F1A was downregulated in cancerous tissue. Conversely, decreased expression of ATP5F1B, C, and E was associated with better overall and recurrence-free survival, while high expression of ATP5F1A and D was associated with good prognosis. Moreover, mutation analysis revealed amplification and over-expression of ATP5F1C and E, which was further validated by protein-level analysis in tumor tissues. Enrichment analysis demonstrated oxidative phosphorylation and ATP metabolism, while TIMER analysis identified subtype-specific immunometabolic roles. Our results reveal ATP5F1C and ATP5F1E as promising prognostic biomarkers in breast cancer and suggest that differential ATP5F1 expression shapes tumor bioenergetics and the immune microenvironment. Crucially, further experimental and clinical validation is essential to clarify mechanistic contributions to breast cancer pathogenesis and to explore therapeutic targeting. These insights may guide personalized interventions exploiting mitochondrial vulnerabilities.