Standards for manual pollen and fungal spore monitoring have been established based on several decades of experience, tests, and research. New technological and methodological advancements have led to the development of a range of different automatic instruments for which no standard yet exist. This paper aims to provide an overview of aspects that need to be considered for automatic pollen and fungal spore monitoring, including a set of guidelines and recommendations. It covers issues relevant to developing an automatic monitoring network, from the instrument design and calibration through algorithm development to site selection criteria. Despite no official standard yet existing, it is essential that all aspects of the measurement chain are carried out in a manner that is as standardised as possible to ensure high-quality data and information can be provided to end-users.