The purpose of this study was to compare the removal efficiencies of manganese (Mn) and iron (Fe) using pristine banana peel biochar (BPB) and phosphoric acid pre-treated biochars (PBPB) derived from banana peels. The removal efficiencies of Mn and Fe were investigated under different adsorbent dosages (0.4–2 g L−1), temperatures (15–45 °C), and ionic strengths (0–0.1 M), and were directly correlated to the differences in physicochemical properties of BPB and PBPB, to identify the removal mechanisms of heavy metals by adsorption processes. The removal of Mn by PBPB obeyed the Freundlich isotherm model while the removal of Mn and Fe by BPB followed the Langmuir isotherm model. However, the removal of Fe by PBPB followed both Freundlich and Langmuir isotherm models. The removal efficiencies of Mn and Fe by BPB and PBPB increased with increasing temperatures and decreased with increasing ionic strengths. PBPB more effectively removed Mn and Fe compared to BPB due to its higher content of oxygen-containing functional groups (O/C ratio of PBPB = 0.45; O/C ratio of BPB = 0.01), higher surface area (PBPB = 27.41 m2 g−1; BPB = 11.32 m2 g−1), and slightly greater pore volume (PBPB = 0.03 cm3 g−1; BPB = 0.027 cm3 g−1). These observations clearly show that phosphoric acid pre-treatment can improve the physicochemical properties of biochar prepared from banana peels, which is closely related to the removal of heavy metals by adsorption processes.