Insights from applied respiratory physiology are essential for tailoring mechanical ventilation strategies to a patient’s lung function. Despite the potential to improve outcomes clinicians do not routinely take full advantage of available lung function tools. This is unfortunate when considering the burden of prolonged hospital stay on critically ill children and their families. In this review we will a) focus on difficult conditions encountered at bedside when evaluating lung function in critically ill and mechanically ventilated children, b) discuss how improved standardisation can enhance reproducibility and detect disease-specific alterations, c) emphasise the impact of operators when assessing respiratory system mechanics, and d) provide suggestions on how to approach lung function related challenges at bedside.