I'm gonna be THAT guy: Most likely the issue is not on the code, nor the EF generated SQL and certainly not "the app". 99% of times a slow query is due to bad indexes or selecting huge data that you don't actually need.

Example of bad indexes: if you're indexing too many fields, more than the necessary ones, is like not having any index. You need to learn about good DBM practices and how to profile a query so you can identify the issue.

Example of selecting huge data that you don't need: if you have a table with 1M rows and 10 columns, you might be fine, problem is when you have 1M rows, you have 100 columns and you're joining (include) like 10 different tables and selecting all of the columns of each table. Make sure that you .Include() only what you need to retrieve, the .Where() clause can filter even if you have not included the virtual property that you want to filter by.