The phrase implies owning up to the consequences of your choices or behavior. He broke the window and has to take his lumps by paying for it.
Pro Tip 2/3
Not Literal
It's a metaphorical expression, not about physical lumps, but about dealing with tough situations. After losing the game, the team had to take their lumps from disappointed fans.
Pro Tip 3/3
Stay Positive
The phrase can imply maintaining dignity or composure while accepting consequences. Despite the harsh criticism, she took her lumps with a smile.