In the past decades, the 'food versus fuel' debate has caused a transition of first-generation biofuels to advanced biofuels. Although the later seems quite promising, due to its sustainability and low GHG emissions qualities, it is still far from deployment. The major hurdles to the deployment of advanced biofuels include technical and economic challenges, which must be overcome in the near future. Extensive R&D is in progress to bridge the gap between the current technological status and commercial venture. To overcome the significant challenges that make the commercialization of advanced liquid biofuels unrealistic, at this moment, is of prime importance. One of the most significant challenges is the technological barriers, which will probably require some more years of extensive R&D efforts to minimize the issues and concerns. This chapter deals with the technological challenges that the liquid biofuels industry is currently facing in the biochemical conversion of second-and third-generation feedstocks to advanced liquid biofuels. A general introduction to the topic includes the types of liquid biofuels categorized under 'advanced biofuels' and their common routes of production namely biochemical and thermochemical. A detailed description of the current technological issues in the biochemical conversion process is presented mainly under the subcategories: improving feedstocks, pretreatment methods, hydrolytic enzymes efficacy and cost, and process integration. The chapter ends with a review of the current status of R&D in biochemical conversion route for advanced liquid biofuels.