About 4% of the global on-farm energy demand of livestock farms is provided by a renewable energy source. Energy system models can assist farmers in making informed decisions on (renewable) energy systems based on their specific goals, such as reducing greenhouse gas emissions (GHGE), minimising investment costs, or lowering long-term expenses. Often, these models only consider operational GHGE from a technology while disregarding embodied GHGE from their manufacturing process, construction stage and end-of-life disposal. In this work, a case study of a pig farm in Belgium is considered to evaluate both calculation methods. Various scenarios, including different sizes and combinations of technologies, are modelled and their influence on investment cost, economic life cycle cost and GHGE over 20 years are assessed. Operational (or grid related) GHGE are calculated, either including or omitting other life cycle GHGE. The technologies considered are photovoltaic panels, solar collectors, hybrid photo-voltaic panels (PVT), wind turbines, heat pumps, lithium-ion batteries, and thermal energy storage water tanks. A reference point or characterisation factor for each technology was obtained from the ecoinvent database. Results are compared to a reference installation, being a condensing boiler connected to Belgium’s natural gas grid and connected to the electricity grid. Among 90,330 simulated scenarios, 84% of GHGE could be reduced when only considering operational GHGE, compared to 73% at most when embodied GHGE are included. Additionally, all considered scenarios decrease operational GHGE, but only 66,301 of them have lower life cycle GHGE. Scenarios involving batteries were particularly affected. In conclusion, energy system models should include embodied GHGE.