Aim: To investigate the relationship of self-reported anxiety levels with the stress biomarker salivary α-amylase, and examine the fluctuations in anxiety during both non-invasive and invasive periodontal therapies.Material and Methods: All participants in this randomised controlled clinical trial completed the Modified Dental Anxiety Scale (MDAS) and 6-item State-Trait Anxiety Inventory (STAI-6) and provided a saliva sample before and after their periodontal assessment. Participants were then randomised to receive either root surface debridement or oral hygiene instruction. MDAS and STAI-6 scores were completed and saliva samples were taken both before and after interventions.Results: There were 20 participants at baseline. Mean salivary α-amylase levels significantly (p=0.02) decreased after periodontal assessment from 77.24U/ml to 63.51U/ml. In phase two, mean amylase levels increased in the intervention group from 62.99U/ml to 74.30U/ml (p>0.05) and decreased in the control group to 59.34U/ml (p>0.05). Changes in both MDAS and STAI-6 were statistically insignificant across all time points and there were no significant correlations between all three variables. Conclusion: Salivary α-amylase levels, MDAs and STAI-6 scores not correlating with each other may be due to the differences between the physiological, cognitive and emotional components of stress experiences in the periodontal setting. When assessing anxiety, future patient care planning and research should consider these aspects separately.