This study analysed the performance of a hot-water pipe (HWP) and fan-coil units (FCUs) in controlling microclimate conditions in a net-zero energy greenhouse (NZEG). The performance of a previously developed TraNsient SYstem Simulation (TRNSYS) model for the NZEG was enhanced to include a crop model and several HWP emission standards, and the improved TRNSYS model was used to analyse heating, ventilation and air-conditioning (HVAC) systems for different greenhouse sizes in the Republic of Korea. Further, an economic analysis was conducted. The model validation showed excellent agreement between the measured and simulated values, with Nash-Sutcliffe efficiency of 0.98. The presence of crop in the simulation model reduced the total heating load by 14.5 MWh and increased the cooling load by 4 MWh. The capacity of the FCU was increased as the outside temperature rose from 33.4[Formula: see text] to 36.4[Formula: see text] in summer, and the diameter of the HWP was decreased from 25A to 10A as the outside temperature rose from −21.7[Formula: see text] to −12.2[Formula: see text] in winter to maintain the greenhouse at the desired temperature of 15[Formula: see text]. Notably, the payback period was reduced by 9 years when the annual savings in heating energy costs and revenue from carbon trading were considered as a part of the net economic cash flow.