Despite previous research having demonstrated the comparative effects of processing instruction and output-based instruction, further investigation is required to examine the relationships between individual differences in cognitive abilities and these instructional types. This study investigated the associations among three instructional approaches and learners’ language aptitude and working memory in acquiring four Chinese classifiers. Eighty-six second language (L2) Chinese learners from one Chinese university were divided into three experimental groups – processing instruction (PI), meaning-based output instruction (MOI), combined instruction (CI) – and a control group. Tests measuring treatment effects included an untimed grammatical judgment test and an oral elicited imitation test. The LLAMA test and a counting span task were employed to assess learners’ language aptitude and working memory respectively. Multiple regression analysis suggested that phonetic coding ability was significantly predictive of the effects of PI and CI groups. Language analytic ability and working memory were not predictive of the effects of any experimental groups. The findings suggest that providing metalinguistic explanations followed by output-based language activities may mitigate learners’ cognitive differences in language analytic ability and working memory.