Pecube is a three‑dimensional thermal‑kinematic model that enables the prediction of thermochronometry data and the investigation of past tectonic and topographic change, using both forward and inverse modelling approaches. However, the problems addressed by Pecube inversions are typically non‑linear and high‑dimensional, such that multiple models can often reproduce the data equally well. Pecube inversions, which involve the evaluation of large numbers of forward models against observations, are performed using the neighbourhood algorithm (NA), enabling guided exploration of the parameter space. Despite more than a decade of applications, practical guidance on how to configure NA–Pecube inversions remains limited. Furthermore, the recent development of a user‑friendly interface for Pecube is expected to broaden its user base and further increase the need for clear guidelines on NA configuration. This contribution aims to provide intuition and general guidance for performing NA–Pecube inversions through a conceptual approach. Although the proposed guidelines remain intentionally broad and do not guarantee optimal performance for user‑specific problems, they are intended to support informed decision‑making and to provide a practical starting point for NA–Pecube inversions. Users are encouraged to explore and adapt NA tuning parameters to their specific modelling objectives and problem settings.