The efficiency of ATR FT-IR spectrometry was compared with recommended methodologies for physicochemical parameters of eighteen samples of Melipona subnitida honey. Significant differences were found between the values obtained using those techniques for hydroxymethylfurfural, ash and electrical conductivity. The results for the other parameters did not differ significantly, suggesting that this rapid and nondestructive methodology may predict parameters usually used to assess honeys’ quality. The effects of different storage conditions (room temperature, fridge and freezer) on the quality parameters of the product stored during 12 months were studied. Darkening of the honey was observed, particularly in the fridge and freezer. However, the changes occurring in the honey kept on the fridge were not statistically different from those occurring in the product kept on the freezer, except for free acidity. The results obtained for the honey stored at room temperature, best way to preserve, differed significantly from those obtained for the honey kept under the other conditions.