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While 'excel at' and 'excel in' are generally interchangeable, I do think there is a subtle distinction.

excel at applies best to specific activities.

He excels at service returns in badminton.

excel in applies best to more general categories or things that cover many activities.

She excels in school.

To me, "She excels at school" sounds thoroughly ungrammatical and would not be uttered by a native speaker. "He excels in service returns in badminton" also sounds a little bit strange but other native speakers than me might use it.