First, communicate openly with both your wife and your friend. Let them know how you feel about the situation. For example, you can say something like 'I trust you both, but it makes me a bit uncomfortable when you are alone together. Just wanted to share my feelings.' Second, establish some basic ground rules. Maybe something like 'If there's any private conversation, please let me know about it later in a general sense.'
You could try to be more involved in their interactions. For instance, if your friend often comes over, make sure you are around most of the time. You can also encourage group activities. Instead of leaving them alone, plan things where all three of you can participate together, like going on a hike or having a game night. This way, there are no opportunities for any inappropriate behavior to occur in secret. Also, build a strong relationship with your wife where she feels comfortable sharing everything with you.
One way is to get to know your friend better in terms of his values and morals. If he has a strong sense of loyalty and respect, it's less likely he would engage in inappropriate behavior. Similarly, strengthen your relationship with your wife. Have regular date nights, talk about your feelings and expectations in the relationship. Make sure she knows that honesty is crucial. Additionally, if there are any signs that make you suspicious, don't ignore them. But also don't accuse without evidence. Have an honest conversation with both parties to clear the air.