Cool-water settings characterize Ordovician occurrences of Phanerozoic ooidal ironstones (POIs), contrasting sharply with the warm and humid climate typical of other POIs. This geological puzzle was deciphered in this study based on a complex suite of Middle-Late Ordovician POIs in South China hosted in tropical sediments of a warm-water origin, and coeval ferruginous ooid-bearing sediments and ferruginous microbialites that accumulated in a relatively cool-water setting. Here, we demonstrate that, despite their different depositional settings, all Ordovician ferruginous deposits of South China share similar petrographic ultrastructures and delta 56Fe isotopic signatures. This suggests that the formation of POIs was not likely controlled by water temperature but instead is attributable to a microbial iron factory, associated with active upwelling generated from frequent cool-water incursions from Gondwana. This model also explains the predominant occurrence of Ordovician ferruginous deposits in cool-water realms in peri-Gondwana. The Darriwilian peak of their abundance corresponds to the onset of an icehouse episode and a paleotropical cold-water tongue that created complex depositional environments across the South China plate.