There are very serious ethical and pragmatic issues in the quantitative and security study of Muslims. From an ethical perspective, many of these studies denigrate and stereotype Muslims. They also treat them as a problem to be solved, justifying and expanding US power. Pragmatically, it can be hard to collect detailed data on security issues in many Muslim countries, making conventional studies difficult. Yet, standard approaches to these problems are faulty. We cannot abandon positivist analysis, as well-done quantitative studies are actually the best tools we have to push back on negative stereotypes of Muslims. At the same time, we cannot ignore important security topics among Muslim states just because the data we have available is not ideal. Instead, I present a two-pronged approach that can address these issues without ignoring crucial aspects of international relations; scholars should follow best methodological practices to avoid ethical issues, and adopt new standards and novel tools to deal with imperfect data.