The principle adjustments recommended for cookies baked at higher altitudes (generally considered to be above 3,000 feet) are to increase the water slightly, to help the dough come together, and to decrease the amount of chemical leavens (baking powder, baking soda) used.
High-altitude baking can be full of unpleasant surprises: cakes that look like they’re rising beautifully suddenly collapse; cookies meant to be chewy and rich end up dry and flavorless. But there is one easy solution, according to cookbook authors Nicole Hampton and Mimi Council: Start with a recipe developed—and tested—at high elevation.
At 9,000 feet and above, preheat oven about 25 degrees above the baking temperature called for in the recipe. As soon as the baked goods are placed inside the oven, lower the heat to the actual baking temperature called for in the recipe. Storing baked goods: At high altitude, baked goods dry out and get stale quickly.
Lower air pressure (at high altitudes) means less weight pressing down on cookie dough. Because of that, leavening agents tend to release gases more quickly at higher altitudes than at normal altitudes. By the time cookies are done, most gasses have expanded and already escaped from the cookies. Bottom line: your cookies flatten.