This work evaluated the effect of orally or nasally administered Lactobacillus rhamnosus CRL1505 on the resistance of immunocompromised protein-malnourished mice to pneumococcal infection. In particular, we aimed to gain knowledge of the mechanism involved in the immunomodulatory effect of L. rhamnosus CRL1505 in malnourished hosts by evaluating its impact on the immuno-coagulative response. Malnutrition significantly increased lung tissue damage caused by Streptococcus pneumoniae infection. Lung damage was associated with a deregulated activation of coagulation and an altered inflammatory response. Pneumococcal colonization of lung and bacteremia were significantly reduced (p < 0.05) in malnourished mice receiving the CRL1505 strain. Moreover, mice repleted with supplemental L. rhamnosus CRL1505 showed the least alteration of the alveolar-capillary barrier and cell damage in lungs after the infectious challenge, especially when the CRL1505 strain was administered by nasal route. Besides, mice treated with L. rhamnosus CRL1505 showed an improved respiratory innate immune response and a lower activation of coagulation. The results of this work indicate that L. rhamnosus CRL1505 is able to beneficially modulate the inflammation-coagulation interaction after respiratory infections in malnourished hosts.