Whole-plant corn untreated (Control) or treated with an inoculant (Lentilactobacillus buchneri, Lentilactobacillus hilgardii, and Pediococcus pentosaceus, INO) was ensiled for 210 days in mini-silos at constant (MS-C) or variable temperature (MS-V) or for 220 days in bunkers. Bunker samples were collected at 50 (D50) and 150 (D150) cm below silo surface. Samples from MS-V and MS-C had similar pH and concentrations of lactic acid, propionic acid, 1,2-propanediol, and ethanol, but different acetic acid content (P = 0.009). Additionally, MS-V exhibited greater bacterial (P = 0.002) and fungal (P = 0.011) richness than MS-C. Inoculation decreased (P < 0.001) lactic acid levels while increasing (P < 0.05) acetic acid, 1,2-propanediol, and fungal richness in both mini-silos and bunker. In bunkers, samples collected from D50 had a lower aerobic stability (P < 0.05) than D150, but inoculation increased (P < 0.05) aerobic stability compared to Control, regardless of sampling depth. The storage temperature of mini-silos did not markedly impact the fermentation profile or fungal community. Overall, inoculation increased acetic acid production and fungal diversity in mini-silos, regardless of the storage temperature, and in bunkers, irrespective of sampling the depth, improving the aerobic stability of D50 and D150 bunker silages after long-term ensiling.