According to the ideal of value-free science, only epistemic values should be included in decisions that scientists make in activities at the core of scientific inquiry (e.g., hypothesis choice). For the last couple of decades several doubts have been raised against this ideal. Many philosophers of science today seem to agree that not only epistemic values but also non-epistemic values such as moral, social or political values can play a substantial role in scientific reasoning and practice (from choosing a research question or a research project to deciding upon a methodology and its boundaries, accepting or rejecting hypotheses, utilizing the scientific results in further contexts, so on.) So far several, somehow related yet different, approaches have been a part of understanding and revealing the role of epistemic and non-epistemic values in science; yet there are still challenging questions regarding the subject. For instance, what should be the new ideal for science? How should other concepts in philosophy of science, such as scientific objectivity or epistemic trust, be understood from this new perspective? This PhD thesis focuses on the philosophical accounts of how scientific reasoning and values interact, and in this respect, seeks to analyze which values (or value influences) are legitimate in science, and how they are epistemically contributive in the production of scientific knowledge without jeopardizing objectivity in science.