This can be caused by a muscle imbalance (Weak quadriceps and strong hamstrings, etc.) Excessive pronation (arch collapsing too much, causing the knee cap to twist side ways) can also be a source of chondromalacia.
There are things you can do to self treat. For example decreasing activity, icing for swelling, even aspirin.
Biking should actually help chondromalacia, not hurt the condition. You should remember to stay off the large chain ring, avoid hills and adjust your saddle so that your knee is only slightly bent at the bottom of the pedal stroke.
Source: About: Bicycling- Beginners Bicycling website/ photo courtesy of GetImage