The accurate quantification of volatile organic compound (VOC) emission rates from porous media to the air is a challenging problem, as measurements are affected by the chemical and physical characteristics of the porous media, and the operating parameters of the sampling device itself. The main objective of this study is to investigate how flux chamber (the most commonly used sampling device) configurations influence emission rate measurement from three selected porous media. Various parameters were studied, including sweep air flow rate, presence of a mixing fan, headspace volume and thickness of media. Controlled experiments focused on the behaviour of two VOCs commonly found in area sources: acetic acid and 1-butanol. Sweep gas flow rate emerged as the most influential factor, inducing turbulence and dilution over porous media surfaces and impacting emission rate measurements more significantly than headspace volume and fan installation. Variations in porous media properties also affected mass transfer, with emissions from coco coir showing higher mass transfer as its porosity and particle size facilitated gas transportation. While behaviour of acetic acid emission through the media supported the diffusion theory, emission of 1-butanol was affected by a combination of factors, highlighting the role of both diffusive and advective transport mechanisms. Understanding how flux chamber setups and porous media properties influence emission rates is crucial for accurately interpreting data. This knowledge also guides the design of studies, especially when investigating complex sources like biosolids and organic-amended soil.