To investigate the effects of a Bacillus-based direct-fed microbial on milk production and related factors, a study was conducted on Holstein cows (n = 28) starting at 90 ± 11 DIM. The cows were divided into two dietary groups: a control group (CON) that received a total mixed ration (TMR), and a Bacillus-fed group (DFM) that received the same TMR along with a Bacillus subtilis product containing two strains (747 and 1781) in equal amounts. The study lasted for 25 wk and included both primiparous and multiparous cows. The cows were housed in a free-stall barn and were provided with ad libitum TMR, which was fed twice a day. Their daily meals and dry matter intake (DMI) were recorded during wk 1–4 and wk 19–25 using electronic feeders. Milk samples were collected weekly during morning and evening milkings and analyzed for milk fat, protein, lactose, and milk urea nitrogen (MUN). Blood samples were also collected weekly and analyzed for plasma glucose, insulin, cholesterol, insulin-like growth factor 1 (IGF1), and progesterone concentrations. Additionally, rumen fluid samples were collected and evaluated for various species of bacteria. One of the key findings was that daily 4 % fat-corrected milk production (FCM) was influenced by the interaction between treatment (DFM vs. CON) and parity (primiparous vs. multiparous), with multiparous DFM cows producing 11 % more FCM compared to CON. The DFM cows also had a higher milk fat percentage (4.41 % vs. 4.02 %) and MUN concentrations were 1.0 mg/dL higher in the DFM group. In terms of blood metabolites and hormones, multiparous DFM cows had lower plasma cholesterol, glucose, and insulin concentrations compared to CON multiparous cows. However, there were no significant differences between the groups in terms of plasma IGF1 concentrations, insulin-to-glucose ratios, and luteal phase plasma progesterone concentrations. The analysis of rumen fluid samples revealed that the abundance of Ruminococcus albus and Fibrobacter succinogenes group I was greater in the DFM cows compared to CON cows. Furthermore, during the periods when feed intake was measured, the DFM cows had a 9 % reduction in feed intake and a 14 % improvement in feed efficiency (FCM per DMI) compared to CON cows. In conclusion, the two-strain Bacillus product used in this study (Certillus) showed potential as an effective direct-fed microbial. It was found to increase feed efficiency and milk production by altering the composition of ruminal microbiota and metabolism in the cows.