Informed understandings of nature of science and scientific inquiry are generally accepted goals of biology education. This article points out central features of scientific inquiry with relation to biology and the nature of science in general terms and focuses on the relationship of students' inquiry skills in biology and their beliefs on the nature of science. The study took place as a part of the German national curriculum project "biology in context." IRT modelling of students' inquiry skills was performed with a sample of 1553 secondary school students. Final analyses on the relation to NOS beliefs were conducted with 218 participants who were in seventh (n = 50), eighth (n = 58) and ninth (n = 110) grades. Students in higher grades showed more advanced inquiry skills in biology and more sophisticated NOS beliefs. Different dimensions of inquiry skills and NOS beliefs correlated positively on a moderate level. Besides science experience and prior achievement, NOS beliefs contributed to the formation of biological inquiry skills. The findings are discussed with respect to implications for teaching and student assessment.