This study investigated L2 learners’ interpretation of quantifier scope, focusing on the influence of individual differences, including L2 proficiency, working memory (WM) and inhibitory control (IC). A picture selection task using the covered-box paradigm (CBP) was conducted with 70 Chinese-speaking learners of English and a control group of 40 native English speakers. The results revealed that inverse scope (IS) posed particular challenges for L2 learners, leading to reduced, non-target-like access. We attribute this difficulty to factors such as negative L1 transfer, limited L2 input and increased processing demands associated with IS compared to surface scope (SS). More importantly, WM and IC significantly influenced L2 learners’ interpretation patterns, with their effects mediated by L2 proficiency. We also observed individual variation in scope interpretations among native speakers, particularly with negatively quantified (NQ) sentences. This variation provides valuable evidence of individual differences in native speakers’ grammatical knowledge and was partly driven by cognitive factors. Altogether, the findings contribute novel evidence for both domain-general and domain-specific mechanisms underlying quantifier scope interpretation in L2 learners as well as in native speakers.