Kazakhstan has implemented numerous policy reforms to improve its research environment since 1991, experiencing both positive changes and critical challenges. In this study, we conduct a comprehensive investigation of the country’s research environment. Our materials include statistical data, science policy reports, bibliometric data from Scopus, and interview responses. Using descriptive statistics and regression analysis, we analyze the country’s publication capacity, key characteristics, and science funding by the government. We critically review significant policy reforms and conduct interviews with subject matter experts. Our findings suggest there has been an increasing number of publications and growth in citations since joining the Bologna process in 2010, and that there is a high positive correlation between the volume of science funding and publication output, development levels across fields of science, and focus from science on commercialization of science. The challenges relate to publishing in international journals, government financing and commercialization, researcher capacity, scientific areas, and international collaboration. Our contributions to scholarly communication and science policy are two-fold. First, we present the relationship between several factors/policies and the research environment. Second, we reveal the main challenges Kazakhstan and its academic community have experienced which can be considered by stakeholders, including the government, academic institutions, researchers, and other developing countries.