Previously, we investigated the impact of a mixed Lactobacillus buchneri, Lactobacillus plantarum, and Lactobacillus casei inoculant on fermentation and aerobic stability of barley silage over two years in 2009 and 2010. In 2009, a classical response to inoculation was obtained with an increase in acetic acid concentration of silage ensiled in both mini- and bag silos. In 2010, this classical response was not observed in mini-silos but was observed in bag silos. The objective of this study was to determine if molecular microbial ecology could explain the differential responses to the inoculation of barley silage between the two years. The Illumina MiSeq sequencing results showed that inoculation increased Lactobacillus and lowered Pediococcus, Weissella, and Leuconostoc in both types of silos in 2009. However, a similar trend was not observed in mini-silos, but was instead observed in bag silos in 2010. Inoculation did not alter the core fungal community in either silo type in either year. Cladosporium, Leptosphaeria, and Cryptococcus were abundant in fresh forage, but were superseded by Pichia and Kazachstania after ensiling. Our results suggest that changes in silage chemistry corresponded to differences observed in microbial ecology. Inoculation may have less impact when using more mature crops with shorter ensiling times.