The flavor, aroma, and color of coffee can be changed due to mechanical damage, reducing its quality. To measure the mechanical behavior of the fruit, compression tests can be performed at different stages of ripeness. In this study, we analyzed the deformation, strain energy, and von Mises stress of coffee fruits at mature, semi-mature, and immature stages under compression forces. Compression in three directions (x, y, and z) was simulated on coffee fruit models using the finite element method. A compression support was applied in the opposite direction to the force application axis. Numerical simulations of the compression process allowed us to verify that the more mature the fruit, greater the associated mean deformation (2.20 mm mm−1, 0.78 mm mm−1, and 0.88 mm mm−1), the lower the mean strain energy (0.07 mJ, 0.21 mJ, and 0.34 mJ), and the lower the mean equivalent von Mises stress (0.25 MPa, 1.03 MPa, and 1.25 MPa), corresponding to ripe, semi-ripe, and immature fruits, respectively. These analyses not only save time and professional resources but also offer insights into how strain energy and von Mises stress affect fruits at different maturation stages. This information can guide machine adjustments to reduce coffee harvesting damages.