The JU Faculty of Biology and Earth Sciences began to function in 1951, but it was officially established by the Polish Ministry of Higher Education on February 11, 1952. The Faculty specializes in natural sciences, such as biology, geography, geology, environmental sciences and molecular biology, which, as a field of science, became a separate faculty in 2002. These sciences have been developing at the Jagiellonian University throughout its many centuries long history. The main stages of their development are described below.

The Jagiellonian University is one of the oldest European centres of natural science. Some essentials of geography and knowledge ofplants, animals and minerals were taught at the Medical and the Philosophical Faculties of the Krakow University as early as in the 15th century. Since 1609 the Chair in Medical Botany, established thanks to the funds provided in 1602 by Jan Zemełka, was part of the Medical Faculty. The 18th century reform of the university implemented by Hugo Kołłątaj brought about the widespread introduction of empirical methods to both teaching and research. The foundation of the Chair in Chemistry and Natural History in 1780 (active since 1783) was of crucial importance, as it acted as a mother unit for many disciplines. Additional facilities, such as the Botanical Garden (the oldest in Poland, founded in 1783) and the Natural History Unit were also created. They laid foundations for the future botanical, zoological and geological museums.

As Poland lost its independence and the university became part of the framework of the Austrian education system, the scope of research conducted by the Chair in Chemistry and Natural History changed several times. Scientific progress of the 19th century resulted in the emergence of some new independent disciplines. The Chairs of Mineralogy and Geognosy (1811), Botany (1847), Geography (1849), and Zoology and Comparative Anatomy (1850) were founded. After 1850 most natural science departments became part of the Faculty of Philosophy. The revolution in biology brought about by the theory of evolution, together with the development of Earth science in the second half of the 19th century and in the early 20th century was followed by further specialization of research. New chairs were founded, including the Chairs in: Anatomy and Physiology of Plants (1875), Comparative Anatomy (1892), Agricultural Chemistry (1891), Anthropology (1908) along with the GeologicalUnit (1886) and the Paleontological Laboratory (1912). In 1913 the former Chair in Botany, with new collections and a brand-new laboratory added then , was raised to the Institute of Botany status. In 1918 the modern Institute of Geography was founded (since 1920 housed in a separate building). In 1945 the Faculty of Mathematics and Natural Sciences was separated from the Faculty of Philosophy (formally established in 1946 by a decree of the Ministry of Education).

The JU Faculty of Biology and Earth Sciences was established by a decree of the Ministry of Higher Education enforcing the division of the Faculty of Mathematics and Natural Sciences, issued on 11 February 1952. In fact, the Faculty began to function in 1951. During the reorganization of the JU structure in 1951-1952, the former Chairs were grouped into Chair Groups,which were soon to be transformed into the modern-day institutes. The three oldest onesare: The Botanical Institute (1913, since 1970 the Institute of Botany), the Institute of Geography (1918, since 2000 the Institute of Geography and Spatial Management), and the Institute of Zoology (1963). The Institute of Molecular Biology (later named after Jan Zurzycki) was established in 1970, the Institute of Geological Sciences was founded in 1972, and the Institute of Environmental Biology started to function in 1977 (since 1999 as the Institute of Environmental Sciences). In 2002, the Jan Zurzycki Institute of Molecular Biology was separated from the Faculty of Biology and Earth Sciences and transformed into the Faculty of Biotechnology, renamed as the JU Faculty of Biochemistry, Biophysics and Biotechnology in 2006.

The world of natural science owes many important discoveries, ideas and theories as well as new areas and methods of research to the Jagiellonian University academics.

Marian Raciborski and Michał Siedlecki rose to fame as tireless and daring explorers of remote wild areas, who conducted research on the flora and fauna of Java Island. The bio-geographers Antoni Rehman and Jan Kornaś distinguished themselves in the study of African plant life, whereas Mieczysław Klimaszewski and Zdzisław Czeppe were widely known as pioneers in the geomorphological and glaciological explorations of Spitsbergen. The JU academics were also among the forerunners of many new academics disciplines, including: anthropology (Izydor Kopernicki), biochemistry (Leon Marchlewski), genetics (Edward Janczewski), physiology of plants (Emil Godlewski Sr), ichthyology (Maksymilian Siła-Nowicki), applied micropaleontology (Józef Grzybowski), and animal psychology (Tadeusz Garbowski).  

Some of the JU academics became widely famous for the discoveries which were vital for the development of certain fields of natural science. They include, among others: Emil Godlewski Jr, who explored insemination mechanisms in different animal groups, regeneration processes, and artificial parthenogenesis, Marian Książkiewicz, who studied sedimentation of flysch rocks, Michał Siedlecki, renowned for his description of the life cycleof protozoa: gregarines and coccidia, which contributed to the explanation of how Plasmodium which causes malaria develops, Maria Skalińska, whose research into columbines shed much light on the genetic basis of specialization, and Jan Zurzycki, famous for his research into the role of photoreceptors in photosynthesis. The academics of the oldest, "classic" disciplines, that is taxonomists, botanists and zoologists have discovered many thousand plant and animal species. The scholars especially distinguished in this field include Władysław Kulczyński, the leading arachnologist of the late 19th / early 20th century, Bogumił Pawłowski, one of the most renowned experts on European alpine plants,  Stanisław Smreczyński, the insect morphologist and the world's leading expert on weevils. Besides, several hundred previously unknown extinct species have been discovered by the JU paleobotanists and paleozoologists.

The role that the Jagiellonian University has played in the exploration of Polish natural environment cannot be overestimated. During the period of the foreign rule from 1795 to 1918 the Krakow academics considered broadening the knowledge about their motherland a patriotic duty. Thanks to their efforts, grand joint publications were created. They included: Flora Polska(Polish Flora), Szata Roślinna Polski (Vegetation in Poland), Atlas rozmieszczenia roślin naczyniowych w Polsce (Distribution Atlas of Vascular Plants in Poland), Fauna Polski (Polish Fauna) Atlas Geologiczny Galicji (Geological Atlas of Galicia), and various thematic atlases of Poland. What has united natural scientists from many different academic fields has been the issue of environmental protection. Its forerunners in Poland were, among others, the internationally distinguished scholars such as: Maksymilian Siła-Nowicki, Marian Raciborski, Michał Siedlecki, Władysław Szafer.

What has largely contributed to the development of natural sciences at the Jagiellonian University have been the multigenerational schools of thought, some of which are still active today. New generations of young scholars have worked under the guidance of "masters", that is professors. The oldest of such traditions date back to the 1860s, when the Krakow Faunistic School was started by Maksymilian Siła-Nowicki and the Krakow School of Geobotany started by Ignacy Rafał Czerwiakowski and later developed by Marian Raciborski, Władysław Szafer and their successors began to function. In 20th century new research traditions emerged, including the Krakow School of Geomorphology originated by Ludomir Sawicki, Jerzy Smoleński, and Mieczysław Klimaszewski, the Krakow School of Plant Cytogenetics and Embriology of Maria Skalińska, the Krakow School of Photophysiology of Franciszek Górski and Jan Zurzycki, the Polish School of Sedimentology of Marian Książkiewicz, and the Krakow School of Physiology and Ecosystem of Władysław Grodziński.         

The legacy of the past, reflected in the rich collections, specialist literature from many different epochs, and the high quality of academic teaching is an invaluable asset to both staff and students of the Jagiellonian University.