The context is
the translation is "he managed to defeat the undefeated queen"
My question is if 土を付ける can be used to mean defeat? My guess is it has something to do with putting them in the ground/soil?
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Okay I found the source. This line seems to come from the anime 『ダーウィンズゲーム』 which I happen to have seen. Please include the source and more context next time if you can. (See this Meta post) The original line is
Yes, 無敗の女王 is the "undefeated queen." 「土を付ける」 seems to come from the term 「土が付く」, as defined in デジタル大辞泉（小学館）
It is a sumo wrestling term that means what you guessed it means, "defeat". The variant used in the anime contains the transitive verb 付ける as opposed to the intransitive 付く, supposedly putting emphasis on the defeat being the result of an active action on the part of カナメ.
土を付ける is an idiomatic phrase derived fron Sumo match. The defeat is sentenced when you fell down onto the ground or you cross the boundery of circle called Dohyo ring in Sumo match.
When the lost one leaves the dohyo ring, you can see his body with dirt. So, an idiom comes from the scene.
無敗 literally means undefeated and should be considered as undamaged. So, 土を付ける is a natural phrase to describe for someone defeating him/her for the first time.