Background: Upper elementary grade students encounter increasingly complex texts with abundant morphologically complex words. Despite the positive effects of morphology-based vocabulary instruction, emergent bilinguals with limited word reading skills may need additional support. Methods: This study investigated the effects of morphological analysis and morphophonemic analysis instruction on the orthographic and semantic learning of morphologically complex academic words. Fourth- and fifth-grade Spanish-English bilingual students (N = 30) in the United States participated in two learning tasks. In learning task one, participants learned two sets of carefully matched derivational words under morphological and whole-word learning conditions. In learning task two, the same participants learned two other sets of words under morphophonemic and whole-word learning conditions. Each learning task included two learning sessions interweaved by meaning recall and spelling production assessments. Cross-classified multilevel regression was used to assess the effects of intervention conditions, child and item predictors, as well as cross-level interactions. Results: Findings showed no significant difference in meaning recall and spelling measures between morphological and whole-word conditions. Students performed significantly better in the morphophonemic condition than in the whole-word condition for both meaning and affix spelling outcomes. The effect of morphophonemic intervention over whole word condition was stronger for younger students and words of lower base frequencies. Student meaning and spelling performance was significantly predicted by their word reading skills. Conclusions: Morphophonemic analysis instruction enhances word meaning recall and spelling of complex derivative words.