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Recent environmental changes due to land-use and climate change threaten biodiversity and the ecosystem services it provides. Understanding the true scope of these changes is complicated by the lack of historical baselines for many of the interactions underpinning ecosystem services, such as pollination, or disservices, such as disease spreading. To assess changes in such services, it is vital to find ways of comparing past and current interactions between species. Here, we focus on interactions between honey bees – one of the world’s most important agricultural pollinators, the plants they visit, and the microbes they encounter in the environment. DNA in honey offers insights into the contemporary interactions of honey bees. Old honey samples could serve to describe honey bees’ interactions in previous decades, providing a baseline against which to assess changes in interactions over time. By identifying the taxonomic origin of plant, bacterial and fungal DNA in fifty-year-old honey samples, we show that plant DNA can reveal which plants honey bees visited in the past. Likewise, microbe DNA records the microbes, including pollinator and plant pathogens, honey bees encountered and possibly spread. However, some differences in the DNA recovered between old and new honey suggest that differences in DNA degradation of different microbes could bias naive comparisons between samples. Like other types of ancient samples, old honey may be most useful for identifying interactions that historically occurred and should not be taken as proof that an interaction did not occur. Keeping these limits of the data in mind, time series of honey may offer unique information about how honey bees’ associations with flowers and microbes have changed during decades of environmental change.