Within the Biodiversity Genomics Europe project, the "High Mountain Systems - Arthropods" case study was designed to evaluate how arthropod communities change along altitudinal gradients in seven selected mountain systems across different countries in Europe, establishing baseline sampling in mountain ranges to track biodiversity shifts associated with climate change. This SOP describes the sampling design and fieldwork methodology for retrieving arthropod bulk samples for metabarcoding analyses. Site selection included five elevation sites of a high mountan system, including representative vegetation of each gradient. Sampling was performed using two Malaise traps placed at a minimum distance of 50 m between each other, collecting a tube with specimens on the same day of the week, during 20 consecutive weeks. The "Biodiversity Genomics Europe | High Mountain Systems - Arthropod sampling with Malaise traps" intends to standarise Arthropod sampling for community monitoring in further projects for mountain systems.