The Discrete Element Method has been widely used to simulate geo-materials due to time and scale limitations met in the field and laboratories. While cohesionless geo-materials were the focus of many previous studies, the deformation of cohesive geo-materials in 3D remained poorly characterized. Here, we aimed to generate a range of numerical ‘sediments’, assess their mechanical response to stress and compare their response with laboratory tests, focusing on differences between the micro- and macro-material properties. We simulated two endmembers—clay (cohesive) and sand (cohesionless). The materials were tested in a 3D triaxial numerical setup, under different simulated burial stresses and consolidation states. Variations in particle contact or individual bond strengths generate first order influence on the stress–strain response, i.e., a different deformation style of the numerical sand or clay. Increased burial depth generates a second order influence, elevating peak shear strength. Loose and dense consolidation states generate a third order influence of the endmember level. The results replicate a range of sediment compositions, empirical behaviors and conditions. We propose a procedure to characterize sediments numerically. The numerical ‘sediments’ can be applied to simulate processes in sediments exhibiting variations in strength due to post-seismic consolidation, bioturbation or variations in sedimentation rates.