This implies that she left the cafe because he got there (perhaps she didn't want to be in the cafe with him) but it would seem from the sentence that he got there just before she left.
To have one happen before the other more clearly, you could say:
"She had left the cafe when he got there" (she leaves before he arrives)
"She was leaving the cafe when he got there" (She leaves at the same time as he arrives)
"She left the cafe after he got there" (she leaves after he arrives)