We studied the recovery of the growth and physiological parameters of Scots pine seedlings after long-term zinc toxicity. The removal of excess zinc from the nutrient solution resulted in the rapid recovery of primary root growth but did not promote the initiation and growth of lateral roots. The recovery of root growth was accompanied by the rapid uptake of manganese, magnesium, and copper. Despite the maximum rate of manganese uptake by the roots, the manganese content in the needles of the recovering plants did not reach control values during the 28 days of the experiment, unlike magnesium, iron, and copper. In general, the recovery of ion homeostasis eliminated all of the negative effects on the photosynthetic pigment content in the needles. However, these changes, along with recovery of the water content in the needles, were not accompanied by an increase in the weight gain of the recovering seedlings compared with that of the Zn-stressed seedlings. The increased accumulation of phenolic compounds in the needles persisted for a long period after excess zinc was removed from the nutrient solution. The decreased lignin content in the roots and needles is a characteristic feature of Zn-stressed plants. Moreover, the removal of excess zinc from the nutrient solution did not lead to an increase in the lignin content in the organs.