This work proposes a novel beat scoring system for quantifying the effects of exhalation and inhalation on the seismocardiogram (SCG) signals in rest and physiologically modulated conditions. Data from 19 subjects during rest, listening to classical music and recovery states were used. First, the SCG and electrocardiogram (ECG) signals were segmented into exhalation and inhalation phases using the respiration signal; and a representative SCG beat for each exhale and inhale phase was constructed using the ECG R-peak locations. Second, the significant differences across the exhalation- and inhalation-induced SCG beats were detected and extracted using the Teager- Kaiser energy operator. Finally, a gradient-based beat scoring system was developed using extreme gradient boosted trees and monotonic mapping. For the rest, classical music and recovery sessions, the area under the receiver operating characteristic curve was found to be 0.978, 0.874, 0.985, respectively. On the other hand, the kernel density estimation distributions of the inhalation and exhalation scores had an overlap of 14.2%, 41.2%, 10.6%, respectively. Overall, our results show that different physiological modulations directly change the effect of respiration on the SCG morphology, thus standardization across the beats should be studied for achieving more reliable and accurate investigation of cardiovascular parameters. Clinical relevance — Such a system can potentially allow for more informed and clinically useful SCG analysis by providing valuable insights regarding the intra-recording variability caused by the respiratory system.