In addition to its core four academic programs, MESA also has initiated special projects that enhance or expand its ability to assist students.

The Learning Loop is a computer-based learning tool that measures student understanding of key math concepts from the California Mathematics Standards. It serves as a diagnostic tool to help teachers improve math learning for individual students. MESA teachers have been important members of the development team.

The Mathematics-Physics-Technology Institutes are pre-college workshops for teachers that integrate math and science learning through the use of technology. The Institutes are a partnership between MESA and the California Math Project, the California Science Project, and the Mathematics Professional Development Institutes.