This study investigated the effects of scaffolds as cognitive prompts and as metacognitive evaluation on seventh-grade students' growth of content knowledge and construction of scientific explanations in five inquiry-based biology activities. Students' scores on multiple-choice pretest and posttest and worksheets for five inquiry-based activities were analyzed. The results show that the students' content knowledge in all conditions significantly increased from the pretest to posttest. Incorporating cognitive prompts with the explanation scaffolds better facilitated knowledge integration and resulted in greater learning gains of content knowledge and better quality evidence and reasoning. The metacognitive evaluation instruction improved all explanation components, especially claims and reasoning. This metacognitive approach also significantly reduced students' over- or underestimation during peer-evaluation by refining their internal standards for the quality of scientific explanations. The ability to accurately evaluate the quality of explanations was strongly associated with better performance on explanation construction. The cognitive prompts and metacognitive evaluation instruction address different aspects of the challenges faced by the students, and show different effects on the enhancement of content knowledge and the quality of scientific explanations. Future directions and suggestions are provided for improving the design of the scaffolds to facilitate the construction of scientific explanations.