We report on differences in the magnetite (111) surface structure when treated in two different ways. Both preparations are done under UHV conditions at elevated temperatures, but in one case the sample is cooled down while keeping it in an oxygen atmosphere. Scanning tunneling microscopy after each of the preparations shows a different apparent morphology, which is discussed to be an electronic effect and which is reflected in the necessity of using opposite bias tunneling voltages in order to obtain good images. Surface x-ray diffraction reveals that both preparations lead to Fe vacancies, leading to local O-terminations, the relative fraction of which depends on the preparation. The preparation under reducing conditions leads to a larger fraction of Fe-termination. The geometric structure of the two different terminations is found to be identical for both treatments, even though the surface and near-surface regions have small compositional changes; after the oxidizing treatment they are iron deficient. Further evidence for the dependence of iron vs. oxygen fractional surface terminations on preparation comes from Fourier transform infrared reflection-absorption spectroscopy, which is used to study the adsorption of formic acid. These molecules dissociate and adsorb in chelating and bidentate bridging geometries on the Fe-terminated areas and the signal of typical infrared absorption bands is stronger after the preparation under reducing conditions, which results in a higher fraction of Fe-termination. The adsorption of formic acid induces an atomic roughening of oxidized magnetite (111) surface which we conclude from the quantitative analysis of the crystal truncation rod data. The roughening process is initiated by atomic hydrogen, which results from the dissociation of formic acid after its adsorption on the surface. Atomic hydrogen adsorbs at surface oxygen and after recombination with another H this surface hydroxyl can form H2O, which desorbs from the surface, while iron ions diffuse into interstitial sites in the bulk.