Lexical bundles use in academic discourse has been explored across numerous dimensions including discipline, genre, register, student proficiency, and language, among others. These studies have resulted in claims about the nature of these different discourses or their authors, and they have been used in EAP instructional practices. Recent studies on methodological considerations in frequency-based lexical bundles research have pointed to variability in results that stem from changes in criteria used in lexical bundle extraction and corpus composition. Following this, the current study explores the impact of methodological variation in lexical bundle extraction from sets of research articles in Linguistics and Biology, with a focus on the extent of disciplinary variation uncovered in lexical bundles use and function. Experiments with varying frequency thresholds and range specifications as well as corpus composition show that results about lexical bundles use in different disciplinary discourses could be more sharply differentiated when certain variables are used, underscoring the variableness in results and the need for caution in interpreting the findings of lexical bundles research. This paper also evaluates claims made in previous lexical bundles studies using the findings from this study. Finally, previous pedagogical applications of lexical bundles research in academic discourse are discussed.