The current trail system at Fort Custer was developed by the Southwest Michigan Mountain Biking Association (SWMMBA). Existing roads within the Park were linked to singletrack loops that were designed from scratch. The Amusement Park was built in 1993, with subsequent construction of The Trenches, Rocks and Roots, Granny's Garden, Crazy Beaver, and the entire Green Loop. Trail markers were purchased and installed by the SWMMBA as well. The Blue Loop was marked using preexisting trails. The Horse Friends group added trail markers to the system in 2005, encouraging equestrians and bikers to ride in opposite directions for improved safety. The Sled Dog group added markers in 2006.
In 2012 a separate equestrian trail system was developed. The Blue Loop is open to all users. The Red Loop and Green Loop are now biking and hiking only. Unfortunately, the Yellow Loop has been eliminated as the current DNR policy is to have equal trail mileage for equestrians and mountain biking. The Blue Loop is the only recommended trail for novice riders, although anyone can ride the Red or Green. Just walk what you can't ride. DNR policy is that you must remain on designated trails; however, if you find that you or your family cannot ride the entire loop, taking a two track road back to your starting point is acceptable as long as it is not an equestrian trail.