Enteroaggregative Escherichia coli (EAEC) causes acute and persistent diarrhea. Its antimicrobial resistance and strong biofilm formation hinder treatment, highlighting the need for new therapies. This study evaluated the antimicrobial efficacy of 1,10-phenanthroline-5,6-dione (phendione) and its copper [Cu(phendione)3](ClO4)2.4H2O (Cu-phendione) and silver [Ag(phendione)2]ClO4 (Agphendione) complexes against planktonic and biofilm-forming EAEC cells. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values were determined for planktonic cells of 35 clinical EAEC isolates, revealing potent antibacterial activity by all test compounds, with Cu-phendione showing the greatest efficacy, followed by Ag-phendione and phendione. Most combinations of Cu-phendione or Ag-phendione with either ampicillin or tetracycline exhibited additive effects through checkerboard assays, whereas time-kill experiments revealed synergistic interactions between the complexes and those classical antibacterial agents. Minimum biofilm inhibitory concentration (MBIC) analysis identified Cu-phendione as the most effective compound for disarticulating biofilm formation (geometric MBIC = 14.61 μM), followed by Ag-phendione (24.69 μM) and phendione (67.08 μM). Notably, Cu-phendione eradicated biofilms in 24 isolates (68.6%), while Ag-phendione and phendione achieved eradication in 11 (31.4%) and 6 (17.1%) isolates, respectively. Furthermore, the test complexes were able to disrupt established mature biofilms, as demonstrated by the crystal violet assay and scanning electron microscopy. In combination therapy, complete biofilm eradication was achieved in all clinical isolates tested when Cu-phendione was paired with cefoxitin, tobramycin, tetracycline, or ciprofloxacin. Collectively, phendione-derived complexes, particularly Cu-phendione, represent promising candidates for the treatment of EAEC infections in planktonic and biofilm-associated states.