The Institute of Education Sciences (IES) and the National Science Foundation (NSF) issued common guidelines that provide a protocol by which the use of particular methodological designs in a line of research inquiry provides evidence for each successive step in the process of bringing any given instructional intervention into practice. Our purpose was to determine if research on two widely used literacy instruction approaches has been conducted at each methodological stage in the IES/NSF protocol and is relevant to identifying the approach as an evidence-based practice. We applied the IES/NSF pipeline-of-evidence guidelines to assess whether practices touted as having a research base for effectiveness have emerged from an accumulation of empirical evidence and identification of conceptual or theoretical frameworks. In mapping the six steps of the IES/NSF protocol onto the shared book reading and reciprocal teaching studies that had met What Works Clearinghouse evidence standards, we found that only reciprocal teaching involved research at each stage in the protocol and only reciprocal teaching was identified as an evidence-based instructional approach by the What Works Clearinghouse. Our results indicate that the IES/NSF pipeline-of-evidence protocol offers a productive approach to identifying evidence-based practices. The different trajectories of research on reciprocal teaching and shared book reading indicates that research at each stage in the protocol is important to the development of an instructional approach that ultimately demonstrates effectiveness in improving student learning outcomes.