Your first problem is that you are supposed to put PIES on windowsills - not soup.
However, if you are determined to place soup on your windowsill, make it two as opposed to just one bowl of soup - leaving enough for a third bowl in a covered pot atop of the stove.
Then (as three friends of mine often do) take a stroll through the forest. Upon your return, you will find that the soup that was left on the windowsill has flies in it, but the soup that remained in the pot is not only "fly free", but also pleasantly tepid.