Genetic sampling from European honeybee (Apis mellifera) hives is a promising repository of terrestrial environmental nucleic acids (eNA) from a range of taxonomic sources. eNA samples from honeybee hives can be used to monitor environments via vegetation assessments and plant pathogen detection, while simultaneously assessing honeybee hive health through the identification of honeybee pests and pathogens. However, there is still limited comparison across the different types of hive samples commonly used for biomonitoring. There is also a need for less invasive sampling methods to facilitate adoption of hive eNA surveillance at scale. The aim of this study was to compare the effectiveness of using non-invasive swabbing of hive entrances with common sample types collected from honeybee hives (honey, pollen, and bees) for eNA detection of various taxa. Using a DNA metabarcoding approach for bacteria (16S), animal (COI), fungi (ITS1), and plant (ITS2) identification, and metatranscriptomic sequencing for virus detection, swabbing was found to provide comparable or better detection of taxa compared with more invasive sampling methods. Swabs were most informative for identifying bacterial and fungal communities, while plant detections were similar between swabs and honey samples. Detection of RNA viral diversity was highest in honey samples, however, swabs also showed good recovery of plant and insect viruses. A minimum of two swab replicates was recommended to increase taxa yield for DNA metabarcoding. Our study suggests that swabbing of hive entrances is a highly effective biomonitoring method for non-invasively collecting hive eNA and delivering comprehensive surveillance for animal, plant and microbial communities in the environment.