Preconditioning by repeated cyclic loads is routinely used in ex vivo mechanical testing of soft biological tissues. The goal of preconditioning is to achieve a steady and repeatable mechanical response and to measure material properties that are representative of the in vivo condition. Preconditioning protocols vary across studies, and their effect on the viscoelastic response of tested soft tissue is typically not reported or analyzed. We propose a methodology to systematically analyze the preconditioning process with application to inflation testing. We investigated the effect of preconditioning on the viscoelastic inflation response of tree shrew posterior sclera using two preconditioning protocols: (i) continuous cyclic loading-unloading without rest and (ii) cyclic loading-unloading with 15-min rest between cycles. Posterior scleral surface strain was measured using three-dimensional Digital Image Correlation (3D-DIC). We used five variables of characterizing features of the stress-strain loop curve to compare the two preconditioning protocols. Our results showed protocol-dependent differences in the tissue response during preconditioning and at the preconditioned state. Incorporating a resting time between preconditioning cycles significantly decreased the number of cycles (10.5 ± 2.9 cycles vs. 3.1 ± 0.5 cycles, p < 0.001) but increased the total time (15.8 ± 4.4 min vs. 51.2 ± 8.3 min, p < 0.001) needed to reach preconditioned state. At the preconditioned state, 2 of 5 characteristic variables differed significantly between protocols: hysteresis loop area (difference=0.023 kJ/m3, p = 0.0020) and elastic modulus at high IOPs (difference=24.0 MPa, p = 0.0238). Our results suggest that the analysis of the preconditioning process is an essential part of inflation experiments and a prerequisite to properly characterize the tissue viscoelastic response. Furthermore, material properties obtained at the preconditioned state can be impacted by the resting time used during preconditioning and may not be directly compared across studies if the resting time varies by 15 min between studies. Statement of significance: Although applying a preconditioning protocol by repeated cyclic loads is common practice in ex vivo mechanical characterization of soft tissues, the tissue response is typically not reported or analyzed, and the protocol's potential effect on the response remains unclear. This is partially caused by lack of a standardized methodology to precondition soft tissues. We present the first systematic analysis of two representative preconditioning protocols used during inflation testing in ocular biomechanics. Our results show protocol-dependent differences in the viscoelastic response during the preconditioning process and at the preconditioned state. Consequently, the analysis of the preconditioning response represents an essential part of mechanical testing and a prerequisite to properly characterize the tissue viscoelastic response. The effect of preconditioning on the preconditioned state response must be considered when comparing results across studies with different preconditioning protocols.