Electrochemical liquid phase transmission electron microscopy (EC-LPTEM) is an invaluable tool for investigating the structural and morphological properties of functional materials in electrochemical systems for energy transition. Despite its potential, standardized experimental protocols and a consensus on data interpretation are lacking, due to a variety of commercial and customized electrical and microfluidic configurations. Given the small size of a typical electrochemical cell used in these experiments, frequent electrolyte renewal is crucial to minimize local chemical alterations from reactions and radiolysis. This study explores the effects of modifying the flow configuration within the liquid cell under experimental conditions relevant for energy applications in aqueous-based electrolytes, revealing how changes in mass transport dynamics drastically influence the electrochemical response of the cell. Two different cell designs are compared: convection- and diffusion-governed. Ex situ and in situ comparative flow experiments show that the diffusion cell mitigates gas bubbles formation and improves removal of gaseous products. The electrodeposition of Zn nanostructures and the characterization of a Cu-based catalyst are presented as proof-of-concept experiments for energy storage and CO