As a consequence of globalization and migration, the number of children receiving literacy instruction in their second language (L2) is high and still increasing. Therefore, teachers need instruction methods that are effective in both L1 and L2 learners. Here, we investigate the effectiveness of a computerized training program combining phoneme perception, phonological awareness, and systematic phonics, in a sample of second-graders (N = 26) instructed in German as L2. Based on prior evidence concerning (1) literacy acquisition in L2 and (2) effects of literacy development on oral language abilities, we expected significant training effects on children’s literacy skills and vocabulary knowledge. The children of the training group worked through the program during school lessons, 20 min per day, for a period of 8 weeks. The controls continued to receive standard classroom instruction. German tests of phonological awareness, reading, spelling, and vocabulary were performed at three time points (pretest, immediate posttest, and follow-up after 9 weeks). Analyses confirmed that improvements in phonological awareness, spelling, and vocabulary between pretest and posttest were stronger in the training group when compared to the controls. For spelling and vocabulary, these effects were still significant at follow-up. Effect sizes were medium to high. For the reading measures, no group differences were found. In sum, the results yield further evidence for the effectiveness of phonics-based literacy instruction in L2 learners, and for the beneficial effects of basic literacy skills on novel word learning.