Neo-formed contaminants (NFCs) are common in many foods, especially those subjected to high-temperature processing. Among these contaminants, products arising from the Maillard reaction, sugar reduction, thermal degradation of polyphenols and lipid oxidation, including acrylamide, furan, furfuryl alcohol, and hydroxymethylfurfural, are consistently linked to potential neoplastic effects. NFCs are found in globally traded commodities like coffee and cocoa, posing a significant risk due to their frequent consumption by consumers. A direct correlation exists between consumption frequency, exposure levels, and health risks. Hence, it's crucial to establish reliable methods to determine levels in both matrices, aiming to mitigate their formation and minimise risks to consumers. This review offers a comprehensive examination, discussion, and identification of emerging trends and opportunities to enhance existing methodologies for extracting and quantifying NFCs in coffee and cocoa. By presenting an in-depth analysis of performance parameters, we aim to guide the selection of optimal extraction techniques for quantifying individual NFCs. Based on the reviewed data, headspace extraction is recommended for furan, while solid and dispersive solid phase extractions are preferred for acrylamide when quantified using gas and liquid chromatography, respectively. However, it is worth noting that the reported linearity tests for certain methods did not confirm the absence of matrix effects unless developed through standard addition, leading to uncertainties in the reported values. There is a need for further research to verify method parameters, especially for determining NFCs like furfuryl alcohol. Additionally, optimising extraction and separation methods is essential to ensure complete compound depletion from samples. Ideally, developed methods should offer comprehensive NFC determination, reduce analysis time and solvent use, and adhere to validation parameters. This review discusses current methods for extracting and quantifying NFCs in coffee and cocoa, highlighting emerging trends and emphasising the need to improve existing techniques, especially for compounds like furfuryl alcohol.