Colper

@Thanos Welcome to the forum! If you open System Settings > General > Login Items, is Alfred included in the "Open at Login" list? I would suggest you remove and re-add (via the [+] button) Alfred to the launch items, just in case there's been some corruption in macOS in the upgrade to Sonoma (which is a fairly common occurrence).
 
If the issue persists, could you please provide your Diagnostics file, which you can get by typing "?diagnostics" into Alfred? You can then email it to our info@ email address so that I can take a look.

I have the same problem. I already rebuilt the Spotlight cache and did a reload and all the other fairy dust things that get recommended. However, they are only temporary fixes or don't work at all, depending on today's weather or some other unknown variable.
 
Spotlight finds my items immediately, Launchbar finds my items immediately, Alfred 2 worked perfect until maybe two weeks ago (I don't have a good event log, but I'd wager that problems started with the newest version). Now, while I can resort to rebuilding my Spotlight cache, it may or may not help and if I have to do that every day then Alfred starts to look not as attractive anymore. Also, restarting is often not possible as this machine is running complex multi-day calculations frequently.

I just upgraded to the latest version of Alfred. However, i see a very large slow down in the search for applications, folders, or files over the previous version. Now, if I type in lets say a folder name "Engineering Metrics", it first comes up with the search google links. After somewhere between 5-10 seconds, my folder will pop up. It is the same for files and applications as well. This problem does not exist if I just got to spotlight and do the search. What can I do to help fix this problem or give you data to reproduce? I am on a 2012 Mac Pro with 16 gb of ram and Mountain Lion.
 
Thanks