This dataset contains time series observations of land surface-atmosphere net ecosystem carbon dioxide exchange (NEE) and supporting micrometeorological observations collected at 13 peatland eddy covariance (EC) flux observation sites located across Wales, Scotland and England. Sites were active at different timescales between 2008 and 2020. The dataset represents a subset of the variables measured at each site. The full range of variables monitored at each location can be accessed via EIDC records and/or by contacting the authors. This work was supported by the Natural Environment Research Council award number NE/R016429/1 as part of the UK-SCAPE programme delivering National Capability.