A diverse microbial community flourishes in honey. The microbial composition of honey may change before honey reserves are used either by European honey bees (Apismellifera) or by humans for consumption. The aim of this study was to determine if the microbiota in Swedish raw honey could be identified to the genus or species-level using Nanopore sequencing, to evaluate technical reproducibility of Nanopore sequencing, and to see if the fungal and bacterial community composition seems to change due to the age of the honey. Results indicate (1) five of five and one out of five fungi positive controls could be identified with the genus level and species level, respectively, with either ligation or tagmentation based library preparation – the latter had more false positives (2) fungal richness of 2019 honey samples plateaued at 20 taxa, whereas 2023 and 2024 samples were still sequencing new taxa at 20 and 32 taxa, respectively (3) Nanopore sequencing led to broadly consistent compositions of the most abundant bacteria and fungi taxa in raw honey, while both technical replicates and PCR replicates featured rare taxa that were unique between replicates. It was concluded that (1) genus-level identification of fungi had most potential to be accurate with the ligation-based Native Barcoding Kit (2) fungi richness was lower in the 2019 honey sample than in more recent raw honey samples (3) Nanopore sequencing is robust at identification of most abundant taxa but an evaluation of rare taxa compositions across technical replicates would require greater sequencing depth.