Noting the important role of motivation in science students’ reading comprehension, this 14-weeks quasi-experiment investigated the optimal timing for implementation of metamotivational scaffolding for self-regulation of scientific text comprehension. The “IMPROVE” metamotivational self-regulatory model (Introducing new concepts, Metamotivation questioning, Practicing, Reviewing and reducing difficulties, Obtaining mastery, Verification, and Enrichment) was embedded at three different phases of secondary students’ engagement with scientific texts and exercises (before, during, or after) to examine effects of timing on groups’ science literacy and motivational regulation. Israeli 10th graders (N = 202) in eight science classrooms received the same scientific texts and reading comprehension exercises in four groups. Three treatment groups received metamotivational scaffolding before (n = 52), during (n = 50), or after text engagement (n = 54). The control group (n = 46) received standard instructional methods with no metamotivational scaffolding. Pretests and posttests assessed science literacy, domain-specific microbiology knowledge, and metamotivation regulation. Intergroup differences were non-significant at pretest but significant at posttest. The “before” group significantly outperformed all other groups. The “after” group significantly outperformed the “during” group, and the control group scored lowest. Outcomes suggested delivery of metamotivational scaffolding as a potentially important means for promoting students’ science literacy and effortful perseverance with challenging science tasks, especially at the reflection-before-action stage for looking ahead and also at the reflection-on-action stage for looking back. More theoretical and practical implications of this preliminary study were discussed to meet the growing challenges in science teaching schoolwork.