In Fall 2016, the School of Engineering at the Massachusetts Institute of Technology (MIT) chartered the New Engineering Education Transformation (NEET) initiative. NEET aims to educate young engineers to build the new machines and systems that will address societal needs of the 21st century. Students enter NEET in their sophomore year and join one of five threads, namely Advanced Materials Machines, Autonomous Machines, Digital Cities, Living Machines, and Renewable Energy Machines. Threads are cross-departmental pathways of subjects and projects in interdisciplinary areas. NEET students earn an SB degree in their declared major as well as a NEET Certificate in their thread, within the usual four-year duration. Enrollment in the program has increased from 28 students in Fall 2017 to 187 in Fall 2020. NEET students practice the 12 NEET Ways of Thinking, which are cognitive approaches for tackling complex challenges. Thus far, we have incorporated the Ways of Thinking into the program curriculum in two ways: (a) standalone Modules on four Ways of Thinking, i.e., Ethical Thinking, Creative Thinking, Critical Thinking, and Learning How to Learn, which were developed, piloted and taught in 32 sessions from Fall 2018–20 by MIT experts from outside of the program; and (b) an elective class last fall that introduced first-year students to the five threads and to four Ways of Thinking, i.e., Creative Thinking, Systems Thinking, Analytical Thinking, and Making. We learned from the emergency teaching pivot last spring and from remote teaching in fall, and now plan to launch another first-year class that will focus exclusively on Creative Thinking and Systems Thinking along with a semester-long challenge as well as introductory learning vignettes covering each Way of Thinking separately. In this paper we describe how the Ways of Thinking were and are being implemented, share key lessons we have learned, and describe our plans for further incorporation and assessment of the Ways of Thinking into the program.