If I took my levothyroxine first, can I take my alendronate after I wait a while?

Do you take Alendronate daily or weekly?
If you take it weekly then No you should not take the Alendronate later in the day .
Take it first thing tomorrow.
If you take it daily then miss todays dose altogether . (Do not take 2 tablets tomorrow - just the 1)
Administration of alendronate with food, medication, juices, mineral water, coffee, or any other beverage will reduce alendronate absorption and efficacy.

Read more: https://www.drugs.com/ppa/alendronate.html#ixzz12NHCejI0