Food additives are in widespread use in the food industry to extend the shelf life of food, improve its organoleptic characteristics or facilitate industrial processing. Their use is not without controversy, which makes regulation and control crucial for food safety and public health. Among food additives, silicone-based antifoaming agents (polysiloxanes or E900) are difficult to analyze and quantify due to their polymeric nature. Currently, there is no official method of quantifying this additive in foods. In this context, nuclear magnetic resonance (NMR) is a quantitative method for speciation analysis of silicon compounds almost without known interferents. In this work, we describe the evolution of the regulation of the E900 additive, discuss different analytic methods quantifying polydimethylsiloxanes (PDMS), and propose a new method based on NMR suitable for analyzing the content of E900 in the form of PDMS in various types of food from dietary oils to marmalades and jellies, among others. The proposed method consists of a previous quantitative concentration of PDMS by liquid–liquid extraction and the monitoring of the quantification using a bis(trimethylsilyl)benzene (BTMSB) standard to control the variability, ranging within 2–7%, depending on the food. This simple, direct, and reproducible procedure for aqueous and lipidic foods may help to monitor and fill a gap in regulatory legislation regarding the E900 additive.