Provitamin A (proVA) carotenoid synthesis and degradation are strongly influenced by environmental factors, including during post-harvest storage. Hypobaric and hyperbaric storages increase the shelf-life of many crops, but their effects on proVA carotenoids are not known. Our aim was to investigate the effects of modifications of atmospheric pressure and composition on α- and β-carotene concentration and bioaccessibility during the post-harvest storage of carrots and sweet potatoes. Vegetables were stored for 11–14 days at 20 °C in the dark in chambers with modified pressure and O2 concentrations. In carrots, α- and β-carotene concentrations increased significantly during storage, but compared to the control, they were significantly lower in hyperbaria (−23 and −26%, respectively), whereas they did not differ significantly in hypoxia and hypobaria. In sweet potatoes, α- and β-carotene concentrations decreased significantly during storage, but neither hypoxia, hypobaria nor hyperbaria led to any significant change compared to the control. There was a significant increase for carrot α- and β-carotene bioaccessibility in hypobaria and hyperbaria, while there was a significant decrease for sweet potato β-carotene bioaccessibility in hypobaria/hypoxia and normobaria/hypoxia (−45% and −65% vs. control, respectively). Atmospheric pressure and composition during the post-harvest storage of carrots and sweet potatoes modified the concentration and bioaccessibility of proVA carotenoids.