Coffee, a source of useful nutrients, is predominantly consumed as an infusion. Because of this, the availability of these nutrients is influenced by their solubility, which could be affected by cultivation methods. This study investigates the impact of Brazilian-regulated organic cultivation practices on manganese. It evaluates total concentration, fractionation, and infusion extractability using semi-selective extraction and flame atomic absorption spectrometry (FAAS) for analysis. The average total manganese concentrations were 45.5 ± 11.2 mg kg−1 in conventional coffee and 64.7 ± 9.2 mg kg−1 in organic coffee. The higher manganese levels in organic coffee may be attributed to soil conditions that are beneficial to organic farming. Principal component analysis revealed distinct differences in manganese fractionation, underscoring the impact of cultivation methods on manganese metabolism and storage. Despite these disparities, the manganese levels in coffee infusions and the fraction available for absorption exhibited no significant variation between conventional and organic cultivation group samples.