Simple SummaryVitamin K3 (VK3) is the most unstable vitamin. Menadione sodium bisulfite (MSB) and menadione nicotinamide bisulfite (MNB) are two commonly used VK3 in animal diets. Micro-capsule and micro-sphere forms of vitamins, provided from encapsulation techniques, have been used in vitamin production, while the effects of these encapsulated forms on the storage stability of VK3 need systematic investigation. Our results show that high temperature-high relative humidity had a negative effect on the recovery of VK3. The retention of MNB was higher than that of MSB in vitamin premixes. VK3 retention was higher in micro-capsule or micro-sphere forms in vitamin premix and vitamin trace mineral premixes during storage.Six types of vitamin K3 (VK3); two sources (menadione sodium bisulfite, MSB; menadione nicotinamide bisulfite, MNB), and three different forms (crystal, micro-capsule, and micro-sphere) were used to determine the retention of VK3 in vitamin premixes (Experiment 1) or vitamin trace mineral (VTM) premixes (Experiment 2) after 1, 2, 3, and 6 months of storage. The retention of VK3 in vitamin premixes was evaluated at 25 °C/60% relative humidity or 40 °C/75% relative humidity in an incubator in Experiment 1 and in VTM premixes (choline chloride: 0 vs. 16,000 mg/kg) stored at room temperature in Experiment 2. The VK3 retention in vitamin premix or VTM premix decreased significantly with the extension of storage time (p < 0.05). In Experiment 1, the VK3 retention was higher in the 25 °C/60% incubator (56%) than in the 40 °C/75% incubator (28%). The MNB retention (52%) was higher than MSB retention (32%). The retention of VK3 in micro-capsules (43%) or micro-spheres (48%) was higher than the crystal form (35%) after six months of storage. In Experiment 2, there was no difference between the retention of MSB (49%) or MNB (47%). The retention of VK3 of micro-capsule (51%) or micro-sphere (54%) was higher than that of crystal form (40%). The VK3 retention was higher in the choline-free group (51%) than in the choline group (47%) after six months of storage. Finally, the predicted equations of VK3 retention with storage time in vitamin premixes or VTM premixes were established. The R2 of the prediction equations was ≥0.9005, indicating that time is an important factor in predicting VK3 retention. In conclusion, the higher temperature-relative humidity, choline had negative effects on VK3 retention during premix storage. MNB retention was higher than MSB during storage of vitamin premix. The encapsulated forms of VK3, micro-capsules and micro-spheres, could improve VK3 storage stability in vitamin premix and VTM premix.