She had coffee at the end of lunch.

Literal

She [topic-は] lunch [possessive-の] end [at-に] coffee [object-を] drank.

昼食の終わりに ('at the end of lunch') uses 終わり (end) as a time marker. コーヒーを飲む ('to drink coffee') is straightforward. The sentence captures a common dining habit — having coffee as a meal-ender.