The enigmatic Pennsylvanian-age (~307 million years ago) fossil strobilus Tetraphyllostrobus is known from just thirty specimens preserved as compressions from the Sydney Coal Basin in Nova Scotia, Canada, and several recently recognized permineralized specimens from the Mazon Creek lagerstätte in Illinois, USA. The characters and relationships of the genus have remained problematic since it was first described as a strobilus with an unusual decussate arrangement of sporophylls thirty years ago. Here, we investigate four Tetraphyllostrobus specimens from the Mazon Creek flora preserved three-dimensionally as partial permineralizations in iron carbonate nodules. We applied x-ray micro-computed tomography and visualization techniques, combined with peels, super-resolution confocal and scanning electron microscopy, to reconstruct and characterize the three-dimensional (3D) form of the strobilus and its in-situ spores. The specimens reveal exquisite morphological and anatomical details, and clearly show that rather than pairs of decussate bracts there are whorls of six bracts at each node that have numerous sporangia in their axils. The in-situ spores are assignable to Columinisporites, a spore genus largely associated with Sphenophyllales. The new morphological assessment of the cone and its spores unequivocally indicates assignment to the Sphenophyllales. Together this work illustrates the value of combining standard approaches with advanced imagery techniques for the 3D reconstruction and systematic placement of long-extinct enigmatic fossil plants.