The determination of chlorophyll fluorescence emission is a powerful tool for assessing the status of PSII and the allocation of absorbed light to photosynthesis v. photoprotective energy dissipation. The development of field-portable fluorometers has enabled growing numbers of scientists to measure fluorescence emission from plants in diverse field settings. However, the ease of operation of contemporary fluorometers masks the many challenges associated with collecting meaningful and interpretable fluorescence signals from leaves exposed to relevant environmental conditions. Here, we offer methodological advice aimed at, but not limited to, the non-specialist for the proper measurement of fluorescence parameters, with an emphasis on avoiding common errors in the use of fluorescence under field conditions. Chief among our suggestions is (1) to delay use of automatically calculated fluorescence parameters, presented by the instrument software, until raw data ‘traces’ have been carefully inspected to ensure the integrity of findings, and (2) to combine chlorophyll fluorescence analysis, as a rapid, preliminary method of assessing plant responses to stress, with additional methods of characterising the system of interest (e.g. gas exchange, foliar pigment composition, thylakoid protein composition).