Anaerobic digestion (AD) is an important technology for achieving sustainability, but it faces challenges in meeting rising production demands while remaining economically profitable. One difficulty is the lack of a comprehensive understanding of the many interactions within anaerobic digesters, which makes it challenging to fully optimize them. This is particularly notable when considering the interlinked dynamics between micronutrient availability and fluid behavior. This study addresses this gap by focusing on key operational parameters affecting the efficiency of the process in continuous stirred-tank biogas reactors, which are the most used AD technology today. It does so by proposing and evaluating a novel conceptual model of the mechanisms behind how different parts of AD processes interact upon disturbance, highlighting strategies for preventing process failure. This article aims to improve our understanding of the complexity of AD biotechnology and to provide a starting point for developing advanced strategies for operational optimization.