The aim of this work was to characterize selected physicochemical parameters, pollen quantity, and microbiological characteristics of six honey samples collected in three northeastern Algerian wilayas (Souk Ahras, Guelma and Annaba) and one commercial honey (Saint Clara brand). The samples were compared using the parameters actually measured: diastatic index, proline, hydroxymethylfurfural (HMF) content, pollen quantity, and yeast and mold loadings. Statistical analyses highlighted important variations between studied samples. The honeys from Souk Ahras generally showed higher pollen quantities, relatively high diastatic index and proline values, and lower HMF and microbial counts, based on the measured parameters. Some Guelma and Annaba honeys and the commercial honey presented higher HMF, yeast and mold counts, indicating less favorable profiles with respect to the measured indicators. Spearman correlation analyses found significant associations between several studied parameters. Positive correlations between HMF and yeasts and negative correlations between diastatic index and yeasts were demonstrated. The results of multivariate analyses (PCA and hierarchical clustering) divided the samples into three groups according to their measured analytical parameters and sampling location. The findings provide that honey quality is depending on several factors among which pollen, physicochemical and microbiological parameters seem to play an important role as quality markers.