Incorporating representations of human decision-making that are based on social science theories into social-ecological models is considered increasingly important – yet choosing and formalising a theory for a particular modelling context remains challenging. Here, we reflect on our experiences of selecting, formalising and documenting psychological and economic theories of human decision-making for inclusion in different agent-based models (ABMs) of natural resource use. We discuss the challenges related to four critical tasks: How to select a theory? How to formalise a theory and how to translate it into code? How to document the formalisation? In this way, we present a systematic overview of the choices researchers face when including theories of human decision-making in their ABMs, reflect on the choices we made in our own modelling projects and provide guidance for those new to the field. Also, we highlight further challenges regarding the parameterisation and analysis of such ABMs and suggest that a systematic overview of how to tackle these challenges contributes to an effective collaboration in interdisciplinary teams addressing socio-ecological dynamics using models.