Windows in churches are often quite large. Sometimes they are too big to fit completely into your frame. Experiment with framing to get around this.
Many people tend to hold their camera horizontally to take pictures, but you can also hold your camera vertically. Most windows will fit better in the frame when your camera is held in this position.
Sometimes including bits of the wall around window will naturally add interest to your picture by framing the window. Sometimes you may only want to include the window in your picture with none of the wall around it.
Look for details in the window that will look good in a picture. Sometimes taking a picture of an entire window doesn’t give you the best results. You can zoom into individual images in the glass and get a more interesting and detailed picture.
You can also deal with windows that are too big by taking separate pictures of different sections of the window and then combining them in an image editing software program.
Try a bunch of different framing options to see what looks best.
When you take a picture of a window you’re usually looking up at it. That will distort the look of the window by making the top of it appear narrower than the bottom. You can avoid this by standing back from the window and using your zoom lens to get a closer picture.
~Stained Glass Window Photography from Digital Photography Advisor