If you have a standard code signing certificate, some time will be needed for your application to build trust. Microsoft affirms that an Extended Validation (EV) Code Signing Certificate allows us to skip this period of trust-building. According to Microsoft, extended validation certificates allow the developer to immediately establish a reputation with SmartScreen. Otherwise, the users will see a warning like "Windows Defender SmartScreen prevented an unrecognized app from starting. Running this app might put your PC at risk.", with the two buttons: "Run anyway" and "Don't run".
Another Microsoft resource states the following (quote): "Although not required, programs signed by an EV code signing certificate can immediately establish a reputation with SmartScreen reputation services even if no prior reputation exists for that file or publisher. EV code signing certificates also have a unique identifier which makes it easier to maintain reputation across certificate renewals."
My experience is as follows. Since 2005, we have been using regular (non-EV) code signing certificates to sign .MSI, .EXE and .DLL files with time stamps, and there has never been a problem with SmartScreen until 2018, when there was just one case when it took 3 days for a beta version of our application to build trust since we have released it to beta testers, and it was in the middle of certificate validity period. I don't know what SmartScreen might not like in that specific version of our application, but there have been no SmartScreen complaints since then. Therefore, if your certificate is a non-EV, it is a signed application (such as an .MSI file) that will build trust over time, not a certificate. For example, a certificate can be issued a few months ago and used to sign many files, but for each signed file you publish, it may take a few days for SmartScreen to stop complaining about the file after publishing, as was in our case in 2018.
As a conclusion, to avoid the warning completely, i.e. prevent it from happening even suddenly, you need an Extended Validation (EV) code signing certificate.