Recurrent laryngeal nerve (RLN) damage in infants leads to increased dysphagia and aspiration pneumonia. Recent work has shown that intraoral transport and swallow kinematics change following RLN lesion, suggesting potential changes in bolus formation prior to the swallow. In this study, we used geometric morphometrics to understand the effect of bolus shape on penetration and aspiration in infants with and without RLN lesion. We hypothesized (1) that geometric bolus properties are related to airway protection outcomes and (2) that in infants with RLN lesion, the relationship between geometric bolus properties and dysphagia is changed. In five infant pigs, dysphagia in 188 swallows was assessed using the Infant Mammalian Penetration–Aspiration Scale (IMPAS). Using images from high-speed VFSS, bolus shape, bolus area, and tongue outline were quantified digitally. Bolus shape was analyzed using elliptical Fourier analysis, and tongue outline using polynomial curve fitting. Despite large inter-individual differences, significant within individual effects of bolus shape and bolus area on airway protection exist. The relationship between penetration–aspiration score and both bolus area and shape changed post lesion. Tongue shape differed between pre- and post-lesion swallows, and between swallows with different IMPAS scores. Bolus shape and area affect airway protection outcomes. RLN lesion changes that relationship, indicating that proper bolus formation and control by the tongue require intact laryngeal sensation. The impact of RLN lesion on dysphagia is pervasive.