The extensive evidence of an ocean over a silicate nucleus makes Europa a candidate for the emergence of a second evolutionary pathway of autochthonous life. We argue that the most urgent question in astrobiology is the origin of habitable ecosystems (a question in geochemistry), rather than the alternative search for the origin of life itself (a question in chemical evolution). Since certain Solar System bodies may share a similar geophysical past with Earth, our more modest approach forces upon us the question: Can available instrumentation be the ‘pioneer’ in the discovery of habitable ecosystems in geophysical environments similar to the early Earth? It will be shown that a central piece in this dilemma is the chemical element sulphur (S). The Europan non-ice surficial elements that distort the water–ice absorption bands were found to be widespread, patchy and, most likely, endogenous. The Galileo Mission discovered these patches, which were subsequently confirmed by the 2007 flyby of New Horizons. We argue that penetrators should be inserted into orbital probes in the future exploration of Jupiter's System. Penetrators provide what could be a key instrument in the exploration of Europa, given the adverse space weather in its environment due to the Jovian magnetosphere and radiation. Indeed, there are alternative views on the radiation-induced S-cycles produced on the surficial molecules that are present on the icy surface; however, S is common to both interpretations. Hence, mass spectrometry should be an essential part of any future payload. The largest S-fractionations are due to microbial reduction and not to thermochemical processes, allowing a test of the hypothesis for the origin of habitable ecosystems. The microbial fractionation of stable S-isotopes argue in favour of penetrators for the survey of the surfaces of both Europa and Ganymede.