Over the past few decades, nanostructured conducting polymers have received great attention in several application fields, including biosensors, microelectronics, polymer batteries, actuators, energy conversion, and biological applications due to their excellent conductivity, stability, and ease of preparation. In the bioengineering application field, the conducting polymers were reported as excellent matrixes for the functionalization of various biological molecules and thus enhanced their performances as biosensors. In addition, combinations of metals or metal oxides nanostructures with conducting polymers result in enhancing the stability and sensitivity as the biosensing platform. Therefore, several methods have been reported for developing homogeneous metal/metal oxide nanostructures thin layer on the conducting polymer surfaces. This review will introduce the fabrications of different conducting polymers nanostructures and their composites with different shapes. We will exhibit the different techniques that can be used to develop conducting polymers nanostructures and to investigate their chemical, physical and topographical effects. Among the various biosensors, we will focus on conducting polymer-integrated electrochemical biosensors for monitoring important biological targets such as DNA, proteins, peptides, and other biological biomarkers, in addition to their applications as cell-based chips. Furthermore, the fabrication and applications of the molecularly imprinted polymer-based biosensors will be addressed in this review.