Recent calls for education research to adopt scientific principles have created much debate in the education research community. There is, however, a general consensus on the value of evidence-based research to guide educational programs and policies. Researchers are, therefore, posed with the challenge of conducting research that is regarded as rigorous and valid, in terms of a scientific inquiry. This paper, reports on how these issues may influence research that is intentionally underpinned by evidence-based research methodology. A research project to investigate students' development of statistical thinking and reasoning in an ICT environment provides an example that illustrates how evidence-based research can shape research practice. This is followed by a description of the development of a student survey and a framework for the evaluation of data-analysis software. Both instruments were based on theoretical frameworks from the literature on statistics education, to strengthen the internal validity of the research. They potentially provide the opportunity to gather reliable and meaningful evidence, and demonstrate the practical application of empirical methods to explore and explain the complexity of real life situations.