Abstract This research investigated the harvest, ambient pre-treatment, and storage of whole-plant corn as an alternative to conventional systems where corn grain and stover are fractionated at harvest. Harvesting the whole-plant, both grain and most of the above ground stover, after physiological maturity can reduce the intense logistics challenges typically associated with corn harvest and expand the harvest window. To determine the feasibility of the proposed system, corn was harvested at 350–840 g kg −1 whole-plant dry matter (DM) using a forage harvester and then ensiled in pilot-scale silos. Ambient pretreatment during storage was investigated using both dilute acid and lime. Both pretreated and control whole-plant silages were very well conserved during anaerobic storage with DM losses generally less than 40 g kg −1 . Hydrodynamic separation of the grain and stover fractions after storage was found to be more effective at fractionating starch and fiber than conventional dry grain harvest, and both fractions had desirable composition. The effects of pretreatment on the silage were very pronounced at 30 and 100 g (kg DM) −1 sulfuric acid loading with less than 100 g (kg DM) −1 of the hemicellulose still bound in the cell wall at DM contents greater than 500 g kg −1 . The whole-plant harvest and storage system was shown to be a viable alternative to conventional corn grain and stover systems for producing feedstocks for biochemical conversion.