Methods for processing substrates in twin chamber processing systems having first and second process chambers and shared processing resources are provided herein. In some embodiments, a method may include flowing a process gas from a shared gas panel to a processing volume of the first process chamber and to a processing volume of the second process chamber; forming a first plasma in the first processing volume to process the first substrate and a second plasma to process the second substrate; monitoring the first processing volume and the second processing volume to determine if a process endpoint is reached in either volume; and either terminating the first and second plasma simultaneously when a first endpoint is reached; or terminating the first plasma when a first endpoint is reached in the first processing volume while continuing to provide the second plasma in the second processing volume until a second endpoint is reached.