Orthography plays a crucial role in L2 learning, which generally relies on both oral and written input. We examine whether incongruencies between L1 and L2 grapheme-phoneme correspondences influence bilingual speech perception and production, even when both languages have been acquired in early childhood before reading acquisition. Spanish–Basque and Basque–Spanish early bilinguals performed an auditory lexical decision task including Basque pseudowords created by replacing Basque /s̻/ with Spanish /θ/. These distinct phonemes take the same orthographic form, <z>. Participants also completed reading-aloud tasks in Basque and Spanish to test whether speech sounds with the same orthographic form were produced similarly in the two languages. Results for both groups showed orthography had strong effects on speech perception but no effects on speech production. Taken together, these findings suggest that orthography plays a crucial role in the speech system of early bilinguals but does not automatically lead to non-native production.