Mobile eye tracking captures egocentric vision and is well-suited for naturalistic studies. However, its data is noisy, especially when acquired outdoor with multiple participants over several sessions. Area of interest analysis on moving targets is difficult because A) camera and objects move nonlinearly and may disappear/reappear from the scene; and B) off-the-shelf analysis tools are limited to linearly moving objects. As a result, researchers resort to time-consuming manual annotation, which limits the use of mobile eye tracking in naturalistic studies. We introduce a method based on a fine-tuned Vision Transformer (ViT) model for classifying frames with overlaying gaze markers. After fine-tuning a model on a manually labelled training set made of 1.98% (=7845 frames) of our entire data for three epochs, our model reached 99.34% accuracy as evaluated on hold-out data. We used the method to quantify participants’ dwell time on a tablet during the outdoor user test of a mobile augmented reality application for biodiversity education. We discuss the benefits and limitations of our approach and its potential to be applied to other contexts.