This research proposes a new product development (NPD) framework for innovation-driven deep-tech research to commercialization and tested it with three case studies of different exploitation methods. The proposed framework, called Augmented Stage-Gate, integrates the next-generation Agile Stage-Gate development process with lean startup and design thinking approaches. The framework consists of six stages and five gates and focuses on critical thinking to help entrepreneurs avoid psychological traps and make the right decisions. Early activities focus on scouting for potential socioeconomically impactful deep-tech research, developing a business case, market analysis, and strategy for problem–solution fit, and then, moving to a build–measure–learn activity with a validated learning feedback loop. Next, suitable exploitation methods are decided using weight factor analysis, developing intellectual property (IP) strategy, completing the university technology transfer process, and participating in fundraising. To pass each gate, the committee board members, consisting of tech, business, IP and regulatory, and domain experts, will evaluate the passing criteria to decide Go/No-Go. Applying the framework to the case studies results in successful university research commercialization. The model, case study, and lessons learned in this paper can be useful for other deep-tech incubator programs to successfully launch deep-tech research for commercialization. The case studies’ positive outcomes validate the Augmented Stage-Gate framework, yet their success is not entirely guaranteed due to external factors like regulatory constraints, entrepreneur characteristics, timing, and the necessary ecosystem or infrastructure, particularly in emerging markets. These factors should be taken into account for future research purposes.