Phytases are widely used food and feed enzymes to improve phosphate availability and reduce anti-nutritional factors. Despite the benefits, enzyme usage is restricted by the harsh conditions in a gastrointestinal tract (pH 2–6) and feed pelleting conditions at high temperatures (60–90 °C). The commercially available phytase Quantum® Blue has been immobilized as CLEAs using glutardialdehyde and soy protein resulting in a residual activity of 33%. The influence of the precipitating agent, precipitant concentration, cross-linker concentration and cross-linking time, sodium borohydride as well as the proteic feeders gluten, soy protein and bovine serum albumin (BSA) has been optimized. The best conditions were 90% (v/v) ethyl lactate as precipitating reagent, 100 mM glutardialdehyde and a soy protein concentration of 227 mg/L with a cross-linking time of 1 h. The intrinsically stable phytase remained its high thermal stability and temperature optimum. The phytase-CLEA achieved a 425% increase of residual activity under harsh acidic conditions between pH 2.2 and 3.5 compared to the free enzyme. The free and immobilized phytase were deployed in an in vitro assay simulating the acidic conditions in the gizzard of poultry at pH 2. The hydrolysis of phytate was monitored using a novel high-performance thin-layer chromatography (HPTLC) analysis and DAD scanner to study the InsPx fingerprint. All lower inositol phosphate pools (InsP1–InsP6) and free phosphate were separated and analyzed. The phytase-CLEA efficiently released 80% of the total phosphate within 180 min, whereas the free enzyme only released 6% in the same time under the same conditions.