I think majority of the good practices are the same in PHp as in other languages like Java, many PHP issues were caused by creating SQL statements using user in

I think majority of the good practices are the same in PHp as in other languages like Java, many PHP issues were caused by creating SQL statements using user input(you can have same issues with beginner devs in most languages), so the best practice is to find a framework that does all the ugly part for you(the logins, session management, routing), there are large and small frameworks , I suggest use a popular one even is not perfect(to avoid the risk of hitting bugs if is not used that much or the risk of it getting abandoned or deprecated), Don't get me wrong, if you need to do one small thing, like for example I had a desktop app and the user could submit feedback directly from the app, then a single PHP file was enough for this case(no dependencies, no frameworks), you get the submitted data, clean it and put it in the database or submit it to a third-party API that can handle it.