Scunthorpe manager Ian Baraclough was left hanging his head in frustration after a fourth successive home defeat as they went down 3-2 to Cardiff.
Bothroyd fired Cardiff in front inside a minute before eight minutes later setting up his strike partner Michael Chopra to make it 2-0.
When Bothroyd then made it 3-0 with a 34th-minute header, Scunthorpe looked in real trouble. But midfielder Kevin McDonald reduced the arrears in first-half stoppage time with a right-foot volley and after 73 minutes the home struck back again with a close-range header from debut loan signing Dany N'Guessan from Leicester.
That threatened to make things interesting until Cardiff struck again six minutes later when a shot from Adam Matthews was deflected home by midfield man Seyi Olofinjana.
Baraclough said: "We spent all week preaching to the players the need for us to get away to a good start, particularly against a team like Cardiff. But we were a goal down inside a minute before any of my players had touched the ball or got anywhere really near it.
"When you're 3-0 down in little more than half an hour a lot of things go through your mind, including the thought of a cricket score. We showed great character to get ourselves back into the game but everything that we did in the second half pales into insignificance after what had gone on before. Our home form really is becoming a problem, we desperately want to do better in front of our own fans."