The combination of a replication crisis, the global COVID-19 pandemic in 2020, and recent technological advances, have accelerated the on-going transition of research in cognitive psychology and neuroscience to the online realm. When participants cannot be tested in-person, data of acceptable quality can still be collected online. While online research offers many advantages, numerous pitfalls may hinder researchers in addressing their questions appropriately, potentially resulting in unusable data and misleading conclusions. Here, we present an overview of the costs and benefits of conducting online studies in cognitive psychology and neuroscience, coupled with detailed best practice suggestions that span the range from initial study design to the final interpretation of data. These suggestions offer a critical look at issues regarding recruitment of typical and (sub)clinical samples, their comparison, and the importance of context-dependency in each part of a study. We illustrate our suggestions by means of a fictional online study, applicable to traditional paradigms such as research on working memory with a control and treatment group.