Initially formed to protect the Golden Stream Corridor Preserve in 1998, the Protected Area Management sub-programme has been an essential component of Ya'axché’s work since its inception. Moreover, Ya'axché’s competence was recognised in late 2008 by the Belize Forest Department when they awarded Ya'axché comanagement of the Bladen Nature Reserve, arguably Belize’s most important terrestrial protected area.

In 2005, Belize produced a National Protected Area System Plan that identified the need to move protected area management efforts away from individual unit-based management to system level management. As this is highly complementary to Integrated Landscape Management, Ya'axché placed its full support behind the System Plan and has been responsible for implementing a large number of its recommendations.

One example of this is Ya'axché’s continuous striving to build the capacity of itself and its partners to manage local protected areas effectively. This has been done partially through a shared training programme which includes the development of Belize’s first "open-source" Ranger Manual open for use or adaptation by any agency within the country. This is complemented by developing and implementing current management plans with full participation from local stakeholders both for its own Protected Areas as well as supporting local partners to do the same.

On the ground the most visible aspect of Ya'axché’s Protected Area Management comes from its ranger team, deployed throughout the Maya Golden Landscape. Although the team focuses on the two protected areas that Ya'axché directly manages, the rangers coordinate closely with and support their counterparts in partner organisations to prevent a wide variety of illegal activities at a landscape level that includes six additional protected areas across half a million acres.

Ya'axché’s Protected Area Management is also greatly assisted by the coordinated Educational Outreach and Economic development activities conducted under its Community Outreach and Livelihoods Programme.