Nowadays, food production systems play a relevant role as the steady increase of global population and food demand. The water-energy-food (WEF) nexus is a suitable approach to tackle resources management associated with these three pillars recognizing synergies and trade-offs. Different approaches have been used in the literature to measure the WEF nexus, being material flow analysis (MFA) and life cycle assessment (LCA), two of the most proven methodologies. The MFA approach is based on the amount of resources consumed, while using the LCA perspective considers all flows of the system (LCA footprints approach) or considering only the flows associated with water, energy, and food pillars as the inventory data (WEF-LCA approach). This manuscript compares the three mentioned approaches to identify their strengths and weaknesses. To do this, a sample of 100 Spanish dairy farms is analysed, where a single WEF nexus index (WEFni) is obtained using Data Envelopment Analysis. Results show that only four farms achieved a WEFni equal to 100 in all approaches, while the main difference between them is the number and type of resources considered for calculating the WEF nexus, which could imply a partial identification of hotspots of food systems.