Academic writing remains a challenging area for English as a Foreign Language (EFL) students because successful academic texts require more than grammatical accuracy. This study aims to uncover EFL students’ challenges in academic writing by examining three interrelated dimensions: linguistic, organizational, and argumentative competence. Employing a qualitative descriptive design, the study analyzed academic essays produced by university-level EFL students. The analysis focused on grammatical accuracy, lexical choice, sentence construction, cohesion, paragraph organization, coherence, thesis development, claims, evidence, reasoning, and counterargument construction. The findings indicate that students’ difficulties extend beyond surface-level linguistic errors. At the linguistic level, recurring problems were identified in grammatical accuracy, vocabulary selection, sentence structure, and cohesive devices. At the organizational level, students experienced difficulties in developing focused thesis statements, maintaining paragraph unity, establishing logical connections between ideas, and structuring arguments coherently. More substantially, argumentative competence emerged as a critical challenge, particularly in transforming general opinions into explicit claims supported by relevant evidence and logical reasoning. The findings further suggest that these dimensions are interconnected: linguistic limitations constrain students’ ability to articulate complex ideas, while weak organizational control reduces the clarity and persuasiveness of their arguments. The study highlights the need for integrated academic writing instruction that moves beyond grammar-focused correction toward the simultaneous development of linguistic resources, textual organization, and argumentative reasoning. Such an approach may provide a more comprehensive foundation for strengthening EFL students’ academic writing competence in higher education.