As Melissa said, having been to Jordan and Egypt, you will get a lot of questions. There's nothing to be concerned about. Be patient and answer all questions seriously, even if they seem to be repetitive or irrelevant. It's routine. They may also do a security search of your luggage. That's also routine.
I have lived in Israel for many years and travel in and out of the country on my Israeli passport. In February I was on a 5-day tour to Jordan. In March, when I flew to France, I was questioned a lot about my visit to Jordan. Last week I flew on El Al from Lisbon to Tel Aviv. They went through every single item in both my checked bag and my carry-on before allowing me to check in for the flight home. That's because I left my packed luggage in storage at my hotel for the day; it was a late night flight. Routine, though the search was more thorough than I'd ever experienced before. I don't know if there was an elevated security threat or if it's because Portugal is a fairly new El Al destination or something else.
It sounds like you are planning to cross at a land border. There are three. Waiting time at the Allenby/King Hussein crossing can be long. It may be preferable to use the northern or southern crossing instead, depending on where you plan to tour in Jordan and in Israel.
What airllne are you planning to fly? You may find it better to visit Israel between the other two countries instead of after. There's a daily flight from Cairo to Tel Aviv. There are 2-3 flights a day between Tel Aviv and Amman. If you fly Turkish Air it probably doesn't matter since there are regular flights to Istanbul.