Background The knowledge on bovine vaccines against respiratory viruses on bronchoalveolar fluid cells is scarce. Objective To compare the effects of a commercial intranasal (IN) and intramuscular (IM) vaccine against bovine respiratory disease (BRD) complex viruses on bronchoalveolar fluid cells of healthy heifers. Methods 21 healthy heifers were assigned to three treatment groups: control (CO, N = 7), intranasally vaccinated (IN) (n = 7), and intramuscularly vaccinated (IM) (n = 7). The IN group received 1 mL of the commercial vaccine in each nostril once containing attenuated BoHV-1, bPIV-3, and BRSV. The IM group was vaccinated with two doses of 2 mL with an interval of 21 days of the commercial vaccine containing attenuated BoHV-1, bPIV-3, and BRSV plus inactivated BVDV. At day 0 (D0), before the first vaccine dose, and at D3, D7, and D21, after the last vaccine dose, airway bronchoscopy was performed to observe local irritation and collect bronchoalveolar lavage fluid (BALF). The bronchoalveolar count, cytological evaluation, bronchoalveolar cell oxidative metabolism, and total bronchoalveolar IgA and IgG were measured. Results The IN vaccine increased neutrophil cellularity at D7 and D21 and total IgA at D3 in BALF. Total IgA in BALF also increased at D3 and oxidative metabolism of bronchoalveolar cells at D21 lowered compared to the CO group. Following IM vaccination there was no alteration of immunoglobulins or cell oxidative metabolism in BALF. Both vaccines reduced the number of alveolar macrophages. Conclusion Both vaccines induced bronchoalveolar inflammation during the establishment of the vaccine immunity, which was more expressive in the IN protocol.