Using Machine Learning (ML) prediction to achieve a successful, cost-effective, Condition-Based Maintenance (CBM) strategy has become very attractive in the context of Industry 4.0. In other fields, it is well known that in order to benefit from the prediction capability of ML algorithms, the data preparation phase must be well conducted. Thus, the objective of this paper is to investigate the effect of data preparation on the ML prediction accuracy of Gas Turbines (GTs) performance decay. First a data cleaning technique for robust Linear Regression imputation is proposed based on the Mixed Integer Linear Programming. Then, experiments are conducted to compare the effect of commonly used data cleaning, normalization and reduction techniques on the ML prediction accuracy. Results revealed that the best prediction accuracy of GTs decay, found with the k-Nearest Neighbors ML algorithm, considerately deteriorate when changing the data preparation steps and/or techniques. This study has shown that, for effective CBM application in industry, there is a need to develop a systematic methodology for design and selection of adequate data preparation steps and techniques with the proposed ML algorithms.