The bioavailability of a drug is closely linked to its solubility, making its early determination essential in drug development. The saturation shake-flask (SSF) method is the gold standard protocol for this, which includes a phase separation step—either by sedimentation, filtration, or centrifugation. This step is critical, as it can directly influence the accuracy of the results. This study investigated the impact of centrifugation parameters—time and rotation speed—on solubility measurements. Additionally, we compared two sample preparation protocols: continuous stirring for 24 h versus 6 h of stirring followed by 18 h of sedimentation before centrifugation. Four model compounds were tested at three pH values using Britton–Robinson buffers. Centrifugation was conducted for 5, 10, or 20 min at either 5000 or 10,000 rpm. Results showed that pre-sedimented samples yielded solubility values closer to sedimentation-only references, while continuous stirring often led to overestimated values, particularly at higher speeds and longer durations. One such example was papaverine hydrochloride, that showed solubility values 60–70% higher than the reference after centrifugation at 10,000 rpm for 20 min without prior sedimentation. Lower standard deviations were observed with shorter, slower centrifugation, with 5 min and 5000 rpm yielding results closest to the reference values.