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This study was aimed at development of freeze drying powders from three types of honeys viz. Robinia pseudoacacia (RSA), Plectranthus rugosus (PR) and multifloral honey (MF) from Kashmir Himalayas of India using whey protein isolate (WPI) and maltodextrin (MD) as drying carriers. The powders were evaluated for physical, morphological and structural characterization. Results exhibited that powders with MD as drying carrier showed significantly higher water activity (aw), hygroscopicity, loose bed porosity (ɛL), tapped bed porosity (ɛT) and mean particle diameter (p < 0.05). While powders produced with WPI as carrier showed significantly higher bulk loose density (DL), bulk tapped density (DT) and glass transition temperature (Tg) (p < 0.05). Colour parameters L* and a* were affected by carrier used however b* was affected by type of honey. Morphological properties (SEM) showed that powders with MD as carrier were more “liquefied”, and agglomerated.FTIR analysis confirmed that there were some additional peaks in powders containing WPI (1500–1600 cm−1)and MD (1076 to 953 cm−1) as carriers exhibited interactions between honey components and carrier materials used.XRD analysis showed that powders with MD as carrier presented amorphous and partially crystalline materials. Thus the results concluded that WPI had higher potential as a carrier for production of honey powders using freeze drying in comparison to MD.