The aim of this study was to determine whether a relationship between periodontal healing and protein intake exists in patients undergoing non-surgical treatment for periodontitis. Dietary protein intake was assessed using the 2005 Block food frequency questionnaire in patients with chronic generalized periodontitis undergoing scaling and root planing (n = 63 for non-smokers, n = 22 for smokers). Protein intake was correlated to post-treatment probing depth using multiple linear regression. Non-smoking patients who consumed ≥1 g protein/kg body weight/day had fewer sites with probing depth ≥ 4 mm after scaling and root planing compared to patients with intakes <1 g protein/kg body weight/day (11 ± 2 versus 16 ± 2, p = 0.05). This relationship was strengthened after controlling for baseline probing depth, hygienist and time between treatment and follow-up (10 ± 2 versus 16 ± 1, p = 0.018) and further strengthened after controlling for potential confounders including age, sex, body mass index, flossing frequency, and bleeding on probing (8 ± 2 versus 18 ± 2, p < 0.001). No associations were seen in patients who smoked. Consuming ≥1 g protein/kg body weight/day was associated with reductions in periodontal disease burden following scaling and root planing in patients who were non-smokers. Further studies are needed to differentiate between animal and plant proteins.