Inventory showing 0 Applications

Did this just start happening all of a sudden, or is this a new Jamf Pro setup? Silly question, but have you checked the Inventory Collection Preferences to make sure collecting applications is in fact enabled? I would think it is, especially if the recon states it's looking for applications, but it's still worth checking to make sure.

If it is enabled, I would disable all other collection settings, like Software Updates, home folder sizes (if it's on), etc and leave just the Application collection on and try again. See if you can get it to work and then selectively start turning other collection items on, doing a recon in between, to see if one of them is affecting this.

Is this a High Sierra computer, and if so, have you updated your database schema file to compensate for Apple's wonky Supplemental Update patch name (it breaks recon)?

https://www.jamf.com/jamf-nation/discussions/25648/high-sierra-supplemental-update-breaks-recon

Same thing happened to me recently, and we're also on 9.101. From my JSS, I unloaded Tomcat, then ran mySQL repair and optimize on the db.

The day before the issue occurred, I did a big deletion of old Advanced Computer Searches, SmartGroups and Extension Attributes - JAMF advised that my clean-up may have orphaned data or otherwise contributed to the db issue

forgot to mention I was also seeing issues in my Policy Dashboard: 0 computers Remaining when Remaining is actually >0. For me, Completed and Failed policy tallies were correct but Remaining was not.

Thanks all for the suggestions, I ended up doing a server reboot as a first step and then when trying to load the JSS it was stuck on "Checking tables to Rename" in the JSS setup progress bar.

I did some research on that and it does looks like a database corruption of some kind that causes that. I'm was going to try the mySQL repair as suggested above but attempted doing a backup with the JSS Database utility first. It looks like as part of the backup it is doing a repair. It has a spinning circle right now for "Repairing table Applications" So that seem it like may be the culprit. I"m going to let that run for a bit and see what happens.

Would that be the same as doing a MySQL repair also, or should I go ahead and do that manually once I get a good backup?

So got some news after the repair, it says "table /jamfsoftware/applications is marked as crashed and last automatic repair failed Error: Corrupt

Thoughts on what to try next to repair?

For me, all pre-High Sierra machines showed 0-Applications.
Tried all the solutions above and also consulted with Jamf support and we didn't find solution for this problem.

Well for me, the fix was actually easy!
Just added new path to Inventory collection settings... "Applications/" and it works now!