Asfaka, fir, flower, forest flowers and orange blossom honeys harvested in the wider area of Hellas by professional beekeepers, were subjected to mineral content analysis using inductively coupled plasma optical emission spectrometry (ICP-OES). The main purpose of this study was to characterize the mineral profile and content of toxic metals such as lead, cadmium and chromium, and investigate whether specific minerals could assist accurately in the botanical origin discrimination with implementation of chemometrics. Twenty-five minerals were identified (Ag, Al, As, B, Ba, Be, Ca, Cd, Co, Cr, Cu, Fe, Hg, Mg, Mn, Mo, Ni, Pb, Sb, Se, Si, Ti, Tl, V, Zn) and quantified. Results showed that the mineral content varied significantly (p
< 0.05) according to honey botanical origin, whereas lead, cadmium, and chromium contents ranged between 0.05–0.33 mg kg−1
, <0.05 mg kg−1
, and in the range of <0.12 to 0.39 mg kg−1
, respectively. Fir honeys from Aitoloakarnania region showed the highest mineral content (182.13 ± 71.34 mg kg−1
), while flower honeys from Samos Island recorded the highest silicon content (16.08 ± 2.94 mg kg−1
). Implementation of multivariate analysis of variance (MANOVA), factor analysis (FA), linear discriminant analysis (LDA), and stepwise discriminant analysis (SDA) led to the perfect classification (100%) of these honeys according to botanical origin with the use of Al, As, Ca, Mg, Mn, Ni, Pb, Sb, Si, Zn and total mineral content. However, the higher lead content in the majority of samples than the regulated upper limit (0.10 mg kg−1
), sets the need for further improvements of the beekeepers’ practices/strategies for honey production.