Unfortunately, far too many American adolescents are unable to read proficiently. The science of reading suggests explicit instruction in both word identification and language processing skills should bolster reading proficiency, but most commercial reading interventions for secondary students focus exclusively on the latter skill area. This study explored the effectiveness of the Lexia PowerUp Literacy program (PowerUp), a digital reading intervention that provides explicit instruction in word identification, grammar, and comprehension. There were 122 sixth-grade students attending low-SES schools who participated in this year-long study. Students who used PowerUp showed significantly greater gains on an assessment of word identification, syntactic processing, and basic reading comprehension skills compared to students using an alternative program that offered opportunities to apply comprehension strategies in the absence of explicit and skills-based instruction. Results demonstrate the value of instruction extending beyond comprehension strategies to incorporate the full complement of skills needed for reading proficiency.