Milk thistle (Silybum marianum (L.) Gaertn.) is a medicinal/oil crop plant that produces dormant seeds at maturity. Seeds are released before harvest into the soil seed bank and hence can cause weed control problems in agricultural ecosystems. So far, information on dynamic changes of dormancy state, viability and persistence of milk thistle seeds in the soil seed bank is lacking. Accordingly, in this study the effects of ex-situ (dry in laboratory) and in-situ (buried in soil) storage conditions on dormancy-break and germination were investigated. Freshly harvested (FH) seeds were tested for germination at constant temperature ranging from 5 to 35 °C under both light/dark and dark conditions with or without GA3. Also, FH seeds were buried in June 2019 at depths of 5, 10, and 20 cm in a field and exhumed after 2–12 months of burial and assessed for germination. FH seeds did not germinate at any test conditions, but GA3 and after-ripening in dry storage increased germination, indicating that seeds have non-deep physiological dormancy (PD). With increased dry after-ripening, the ceiling temperature for germination (30 °C) did not change but the base temperature for germination decreased to 5 °C, i.e, seeds exhibited type 2 non-deep PD. Increased seed burial depth increased the length of the in situ after ripening period necessary for complete dormancy alleviation. Furthermore, persistence of seeds in the soil was affected by burial depth. Seeds buried at 5 cm had a transient seed bank and those at 10 and 20 cm a persistent seed bank.