Childhood maltreatment has been associated with significant impairment in social, emotional and behavioural functioning later in life. Nevertheless, some individuals who have experienced childhood maltreatment function better than expected given their circumstances. Here, we provide an integrated understanding of the complex, interrelated mechanisms that facilitate such individual resilient functioning after childhood maltreatment. We aim to show that resilient functioning is not facilitated by any single 'resilience biomarker'. Rather, resilient functioning after childhood maltreatment is a product of complex processes and influences across multiple levels, ranging from 'bottom-up' polygenetic influences, to 'top-down' supportive social influences. We highlight the complex nature of resilient functioning and suggest how future studies could embrace a complexity theory approach and investigate multiple levels of biological organisation and their temporal dynamics in a longitudinal or prospective manner. This would involve using methods and tools that allow the characterisation of resilient functioning trajectories, attractor states and multidimensional/multilevel assessments of functioning. Such an approach necessitates large, longitudinal studies on the neurobiological mechanisms of resilient functioning after childhood maltreatment that cut across and integrate multiple levels of explanation (i.e. genetics, endocrine and immune systems, brain structure and function, cognition and environmental factors) and their temporal interconnections. We conclude that a turn towards complexity is likely to foster collaboration and integration across fields. It is a promising avenue which may guide future studies aimed to promote resilience in those who have experienced childhood maltreatment.