Instructed second language acquisition (ISLA) is one of the fastest growing areas of applied linguistics. With this tremendous potential comes great responsibility for robust, ethical, and transparent research methods that are responsive to and tailored for the ISLA domain. This article highlights unique characteristics of ISLA research, provides a current landscape of methodological trends within ISLA, and makes specific recommendations for research methods in future ISLA studies. I begin by briefly operationalizing ISLA and articulating some of the main research questions and overarching goals within ISLA, as well as the nature and ultimate aims of ISLA research. Next, the most unique methodological challenges for ISLA research are reviewed, including the use of intact classes and heterogeneous small participant pools, cross-sectional studies, using one’s own students for research, and individual differences. This is followed by a discussion of several current trends in ISLA research methods, including examining the process of learning/development, conducting practice-based research, expanding our conceptualization of instructional contexts, replication studies, especially with bi/multilingual learners in diverse contexts, refining our methods with an eye for ethics and justice, equity, diversity, and inclusion, and conducting open, transparent research that has potential for real-world impact and which dialogues with multiple stakeholders at all stages. I conclude by highlighting that, as ISLA continues as an independent research domain, the development and implementation of strong research methods tailored for ISLA is critical for research integrity and to make the greatest strides in understanding language acquisition processes and effective pedagogical interventions in diverse instructional contexts.