Mini-EUSO is a small orbital telescope with a field of view of $44^{\circ}\times 44^{\circ}$, observing the night-time Earth mostly in 320-420 nm band. Its time resolution spanning from microseconds (triggered) to milliseconds (untriggered) and more than $300\times 300$ km of the ground covered, already allowed it to register thousands of meteors. Such detections make the telescope a suitable tool in the search for hypothetical heavy compact objects, which would leave trails of light in the atmosphere due to their high density and speed. The most prominent example are the nuclearites -- hypothetical lumps of strange quark matter that could be stabler and denser than the nuclear matter. In this paper, we show potential limits on the flux of nuclearites after collecting 42 hours of observations data.