A great burden is put on healthcare systems by dental caries and understanding patients’ treatment needs is of utmost importance. The aim of this pre–post study was to assess dental anxiety and the psychological stress induced by two different types of dental treatment (prophylaxis and cavity preparation), by combining psychometric evaluations with salivary biomarkers, in a group of 28 schoolchildren presenting in a university clinic. Pre- and post-treatment unstimulated whole saliva was collected and levels of cortisol, alpha-amylase (sAA) and total protein content were measured. The State–Trait Anxiety Inventory for Children and the Frankl Behaviour Rating Scale (FBRS) were applied. Statistical analysis was performed using the Stata/IC 16 (StataCorp) programme. All salivary parameters showed strong positive correlations between pre- and post-treatment levels. Post-treatment, salivary cortisol decreased (p = 0.008, paired t-test), sAA did not change significantly (p = 0.572, sign test), while the sAA/cortisol ratio (AOC) increased (p = 0.036, sign test). There were no correlations between state and trait anxiety levels. State anxiety scores registered significantly higher values for children with an FBRS score of 3 compared with a score of 4 (p < 0.001, unpaired t-test). The post-treatment decrease in the salivary cortisol level was higher for prophylaxis compared with the cavity preparation group (p = 0.024, t-test). These results demonstrate that sAA and cortisol levels are altered differently by psychological stress induced by two different types of dental treatment.