Recent data indicate that only 34% of American eighth grade students are able to demonstrate grade-level proficiency with academic reading tasks (NCES, 2011). The staggering nature of statistics such as this is even more profound when considering that high level literacy skills combined with mastery of digital texts have become practical requirements for success in secondary education, post-secondary education, and virtually all vocational contexts. Despite this incongruent scenario, little research has been conducted to evaluate instructional methods and reading comprehension strategies with digital texts. To address this critical issue, the present study examined the effects of a metacognitive reading comprehension instructional protocol (STRUCTURE Your Reading (SYR); Ehren, 2008) with eighth grade students using digital texts in a standard social studies classroom in an urban American school setting. The focus of the protocol was on teaching strategies and self-questioning prompts before, during, and after reading. The study employed a randomized controlled design and consisted of three conditions with a total of 4 participating teachers and 124 participating students. The study was conducted over 25 instructional days and two instructional units with 13.83 treatment hours within the standard, social studies classes. Hierarchical ANCOVA analyses revealed that when controlling for pre-test measurements, the comparison and experimental groups performed significantly better than the control group with instructional unit test scores (Unit 2), reading strategy use in all stages of reading (before, during, and after), and self-questioning prompts during reading. Comparison and experimental groups did not significantly differ in these gains, indicating that this instructional protocol is effective with both paper and digital text. These findings suggest that the SYR instructional protocol is effective with secondary students in content area classrooms when using digital text. Furthermore, they suggest that metacognition and reading comprehension strategy instruction are able to be successfully embedded within a content area class and result in academic and metacognitive gains. Clinical implications and future research directions and are discussed.