Jurassic hot-spring chert deposits in the Deseado Massif, Patagonia, Argentina, have been known for over two decades, but the associated biota has only begun to be documented recently, and thus far only from a small number of localities. Here we report the discovery of a large complex of well-exposed Upper Jurassic epithermal siliceous deposits represented by organic-rich cherts preserved within the geothermal system from La Bajada, Santa Cruz, Argentina. The chert samples analyzed so far contain exceptionally well-preserved, in situ and transported, tri-dimensionally silicified plants, animals and microorganisms. Plants include equisetaleans (Equisetum thermale), ferns and gymnosperms. Among them, well-preserved in situ osmundaceous rhizomes in different developmental stages are the dominant component of the taphoflora. Conifers are represented by wood, seeds, leaves and pollen tentatively assigned to the families Araucariaceae and Cheirolepidiaceae. The assemblage also contains vegetative and reproductive structures of fungi, oomycetes, cyanobacteria, algae, testate amoebas, ciliates and numerous remains of unresolved taxonomic affinity. Microorganisms are preserved isolated in the chert matrix or directly associated with plants and other organic remains in mutualistic, parasitic and saprotrophic engagements. Also present are numerous coprolites and arthropod remains that, along with the named microorganisms, are indicative of trophic relationships in the ecosystem. Altogether, this fossil assemblage suggests that distal paleoenvironments within the geothermal system are preserved at La Bajada. The diversity, abundance, and exceptional preservation of fossils in the La Bajada ecosystem provides a unique window into the geological past that offers a substantial contribution to the reconstruction of middle Mesozoic terrestrial ecosystems.