I have done both ways. I have stopped quilting just before the embroidery, but I have also quilted over the embroidery - - I used the invisible thread and it disappeared on the pattern. The embroidery section was too large to not quilt at all.. I was afraid that I wouldn't like it without quilting. I was happy with how the invisible thread quilting turned out. BUT I can understand that not every embroidery motif would work well with quilting