See progress of Spotlight re-indexing in El Capitan Other Questions and Answers address how to check the progress of Spotlight rebuilding its index, previous to El Capitan: Click the Spotlight menu. The menu/panel that appears reports a progress bar if re-indexing is in progress.

In El Capitan, that menu/panel no longer appears. Now a grey box appears in the middle of the screen where we are expected to enter our search words. The re-indexing progress bar no longer appears.
Type something — anything — in the gray box to reveal indexing progress: