With high pozzolanic reactivity, metakaolin (MK) is a popular supplementary cementitious material (SCM), which can be used to partially replace Portland cement in concretes. Due to its small particle size, however, MK can agglomerate, resulting in a nonuniform matrix and underperformance of the produced concrete. To address this issue, this paper exploits a low-cost, bio-based admixture—black tea extract (BTE)—to replace the traditional petroleum-based chemical admixture to enhance the dispersion and workability of MK blended cement mortars. Major biomolecules in the BTE such as caffeine, catechin, theanine, and theaflavin are rich in polyphenol, hydroxyl, and carboxylic acid groups, which can interact with cement particles and have profound effects on the hydration process and microstructure of the hydration products. Experimental studies showed that BTE does improve the workability of the MK blended cement mortar. More importantly, the BTE introduces significant change on the microstructure of the hardened pastes. Both the pores with size less than 50 nm and the total porosity of the hardened paste were significantly reduced, leading to a significant improvement in the micro- and macro-mechanical properties of the hardened paste. Experimental results suggest that up to 35% greater improvement in the compressive strength at 28 days was achieved using the proposed bio-admixture. Economic and environmental advantages of using the BTE as a renewable admixture were also illustrated through analyzing the cost–benefit, embodied carbon, and eco-efficiency of the MK blended mortars.