Furaneol is a widely used flavoring agent, which can be naturally found in different products, such as strawberries or thermally processed foods. This is why it is extremely important to detect furaneol in the food industry using ultra-sensitive, stable, and selective sensors. In this context, electrochemical biosensors are particularly attractive as they provide a cheap and reliable alternative measurement device. Carbon nanotubes (CNTs) and silver nanoparticles (AgNPs) have been extensively investigated as suitable materials to effectively increase the sensitivity of the biosensors. However, a comparison of the performance of biosensors employing CNTs and AgNPs is still missing. Herein, the effect of CNTs and AgNPs on the biosensor performance has been thoughtfully analyzed. Therefore, disposable flexible and screen printed electrochemical aptasensor modified with CNTs (CNT-ME), or AgNPs (AgNP-ME) have been developed. Under optimized conditions, CNT-MEs showed better performance compared to AgNP-ME, yielding a linear range of detection over a dynamic concentration range of 1 fM–35 μM and 2 pM–200 nM, respectively, as well as high selectivity towards furaneol. Finally, our aptasensor was tested in a real sample (strawberry) and validated with high-performance liquid chromatography (HPLC), showing that it could find an application in the food industry.