Extrusion is a continuous, thermo-mechanical process that is common in food industries. In most applications, the feed material is dry particles. Thermal energy and mechanical strain is applied upon extrusion enabling the specific structural transformation of the feed material; for example, texturization by pasting or puffing of starch. Extrusion and transformation of high moisture (≈50%) gel particles like casein-based gels to isotropic or anisotropic structures by, for example, 3-D print, is a major challenge of plant engineering (hygienic design, CIP) and processing. Extrusion instabilities as melt fracture or phase separation are prone to occur when exceeding a certain strain during extrusion of high moisture particles. Hence, extrusion of directly acidified casein-based gel particles was researched in small scale experiments to generate specific semi-hard isotropic or anisotropic matrices. Standardized cheese milk (3.4% protein, 3% fat) was directly acidified by addition of organic acidulants to different pH values (5.5 – 6.3) to vary calcium levels. Casein-based gel particles with different calcium levels (15.8 ± 0.9 to 31 ± 2 mg Ca g⁻¹ protein) were produced by rennet-induced coagulation to investigate thermo-rheological properties and shear behavior at large strain to design hot-melt extrusion. The gel-sol transition temperature (51.7 ± 0.2 to 60 ± 2°C) significantly (P < 0.001) decreased with declining calcium levels. Hence, extrusion die temperature was set to 60°C in capillary rheometer experiments to mimic hot-melt extrusion. The extrudate strands were evaluated visually and recorded pressure profiles were analyzed to determine critical shear rates. It was demonstrated that critical shear rate (10 to 30 s⁻¹) increased significantly (P < 0.001) with decreasing calcium levels. By exceeding the critical shear rate, extrusion instabilities occurred indicating limitation of extrusion. Hence, optimal extrusion process parameters were determined and should be considered to design hot melt extrusion of high moisture gel particles.