Saddle position and cleat adjustment are the two primary areas of concern when treating knee pain from cycling.
The most common cause of patellar tendonitis is a seat that is too low. Raising the seat so that your leg is near full extension (about 15 to 30 degrees of knee flexion is ideal) at the bottom of your pedal stroke will relieve pressure on the patellar tendon.
A seat that is too far forward could also be the culprit. The aggressive angle of the knee in relation to the pedal can put undue stress on the knee joint. By sliding your saddle back, you change this angle. Small adjustments can make a world of difference.
Lastly, the position of shoe cleats plays a significant role in the stress placed on the patellar tendon. Much like the fore/aft adjustment of your seat, the cleat’s fore/aft position must be properly aligned.
It’s a general rule that the pedal axle should be directly underneath the ball of the foot (large bone in forefoot on big toe side). If you are experiencing pain, start with the cleat in this position. From here you can move the cleat slightly forward towards the toe, which will help to put the knee angle in a more favorable position.