The present invention is related to the field of semiconductor processing equipment and methods and provides, in particular, methods and apparatus for in-situ removal of undesired deposits in the interiors of reactor chambers, for example, on chamber walls and elsewhere. The invention provides methods according to which cleaning steps are integrated and incorporated into a high-throughput growth process. Preferably, the times when growth should be suspended and cleaning commenced and when cleaning should be terminated and growth resumed are automatically determined based on sensor inputs. The invention also provides reactor chamber systems for the efficient performance of the integrated cleaning/growth methods of this invention.