Through his extensive visits to all the various ecosystems of Santa Cruz County for his insect and plant collection work, Morgan discovered more and more rare and diverse habitats that were in danger of being developed and in need of protection. The destruction of much of the sandhills inspired Morgan to be involved with local conservation efforts. After helping to start the Santa Cruz Chapter of the California Native Plant Society, he found others who wanted to help. Their advocacy involved writing letters to land developers and government officials, educating the public through slideshows, and attending public meetings.

Through decades of advocacy, his efforts paid off.  Along with others, Morgan was involved in protecting many local habitats, including Quail Hollow Ranch, the Bonny Doon Ecological Reserve, the UCSC Campus Natural Reserve, Moore Creek, Wilder Ranch, Arana Gulch, and Pogonip. In 2008, a small part of the sandhills was officially protected when the Land Trust of Santa Cruz County established it as the Randall Morgan Sandhills Preserve.