The poor biomass titer and biodiesel productivity under natural sunlight are the major challenges for commercialization of algae-biodiesel. Apart from engineering the nutritional medium and CO2 input strategies, the photobioreactor (PBR) design needs high attention to increase light utilization efficiency. Hence, a novel bubble-driven internal mixer was designed for providing frequent light/dark fluctuation which can improve light utilization efficiency and installed in a bubble-column PBR (BC-PBR) to improve productivities of biomass and biodiesel from Chlorella sp. Without any extra energy requirement (via aeration), in 10 L scale BC-PBR with mixer under simulated sunlight, the productivities of biomass and biodiesel were increased by 13% and 62%, respectively, compared to without mixer. Under natural sunlight, the improvement of biomass productivity was 33% with mixer arrangement and final biomass of 8.6 g L−1 was achieved. Further to improve biodiesel productivity and quality under natural sunlight, the lipid induction was started right after the algae growth of 4.2 g L−1 (at the time of highest biomass productivity, 1.4 g L−1 day−1). Consequently, a very highest biodiesel productivity of 753 mg L−1 day−1 (induction-phase) was achieved. To the best of authors knowledge, this is the first study to report bubble-driven mixer in microalgae cultivation technology.