Background/Objectives: The aim of this study is to investigate the association between physical and chemical digestion and nutrition markers (serum albumin (ALB), prealbumin (PAB), and vitamin B12 (B12) levels). Methods: During a detailed checkup at Fujita Health University, we examined the associations of physical (occlusal force, masticatory performance, and swallowing ability (via the 10-item Eating Assessment Tool, EAT-10)) and chemical (Helicobacter pylori (HP) eradication history, HP antibody levels, and oral antacid (proton pump inhibitors) use) digestion parameters with serum ALB, PAB, and B12 levels in 92 individuals (M:67, F:25). Results: Forty-eight percent of the participants were older than 65 years of age, 19% had decreased occlusal force, 3.2% had decreased masticatory strength, 3.2% had decreased swallowing function, 24% had a history of HP eradication, 23% were HP antibody positive, and 16% were taking oral antacid medication. Additionally, 14% and 11% of the patients had low serum ALB and PAB levels, respectively, and 14% of the patients had B12 deficiency. Multivariate analysis adjusted for age, sex, body mass index, and C-reactive protein levels revealed that there were no significant associations between the physical digestion parameters and the serum PAB, ALB, or B12 levels. On the other hand, there was a significant association between oral antacid use and PAB levels (β = −3.3, p = 0.04). Independent of physical or chemical digestion parameters, serum PAB and B12 levels were significantly associated with protein and B12 intake, respectively. Conclusions: Oral antacid use may decrease serum PAB levels, indicating protein synthesis.