Polyphenols represent an important component of soil organic matter (SOM) that widely originates from plants. Birnessite, a ubiquitous manganese (Mn)-oxide, effectively facilitates the oxidative decomposition and polymerization of polyphenols. However, the impact of pH and molecular structure of polyphenols on such processes, as well as the characterization of the degradation products, has not been fully elucidated. Therefore, we performed batch sorption experiments under environmentally relevant pH conditions to investigate the interactions between birnessite and two polyphenol isomers: catechol and hydroquinone. Results revealed that catechol was more effective in reducing Mn and dissolving Mn-oxide than hydroquinone, particularly under lower pH conditions. Correspondingly, a greater amount of carbon was lost from the aqueous system due to sorption and/or oxidative decomposition during catechol reactions than hydroquinone. Spectral data support the concomitant formation of polymers and aliphatic degradation products for both compounds studied. Moreover, lower pH conditions increased the degree of oxidation and proportion of low-molecular-weight species formed. The ortho positioning of hydroxyl groups in catechol facilitated more effective complexation and electron transfer to birnessite than the para configuration of hydroxyls in hydroquinone. This study provides valuable insights into the potential pathways of organo-mineral associations involving Mn-oxides and their role in (de)stabilizing SOM.