Purpose: Second-generation antipsychotic medications (SGAs) are widely used in child psychiatry. SGA-induced metabolic disturbances are common in children, but monitoring practices need systematisation. The study’s aims were to test an SGA-monitoring protocol, examine the distributions of metabolic measurements compared to reference values in child psychiatry patients, and determine whether using a homeostasis model for the assessment of insulin resistance (HOMA-IR) and triglyceride/high-density lipoprotein (TG/HDL) ratio could improve the detection of increased cardiometabolic risk. Materials and methods: A systematic monitoring protocol was implemented. Weight and height, blood pressure, fasting glucose, insulin, HDL, and TG were measured at baseline and four times during follow-up. HOMA-IR, TG/HDL ratio and zBMI were calculated. Age-, gender- and BMI-specific percentile curves for HOMA-IR were used to define elevated cardiometabolic risk. Results: The study patients (n = 55, mean age 9.9 years) were followed for a median of 9 months. A disadvantageous, statistically significant shift, often appearing within the reference range, was seen in zBMI, TG, HDL, glucose, insulin, HOMA-IR, and TG/HDL ratio. The increase in HOMA-IR appeared earlier than individual laboratory values and was more evident than the TG/HDL ratio increase. An HOMA-IR cut point of 1.98 resulted in a sensitivity and specificity of 83%. Compared to a previous study performed in the same location, the monitoring rates of metabolic parameters improved. Conclusion: The monitoring protocol implementation improved the monitoring of metabolic parameters in child psychiatric patients using SGAs. Using HOMA-IR as part of systematic SGA monitoring could help detect metabolic adverse effects.