Ecosystems with dry soils are particularly sensitive to climate changes and anthropogenic actions, which represents a threat to the survival of many cactus species. Ex situ seed conservation strategies should be adopted to support in situ conservation. This study evaluated the effect of conservation conditions on germination and vigor of seeds of Pilosocereus pachycladus subsp. pernambucoensis and Tacinga inamoena. The seeds were packaged in paper bags and glass containers and stored under controlled (8 ± 1 °C; 56 ± 2% relative humidity) and non-controlled (24 ± 2 °C; 75 ± 5% relative humidity) environmental conditions for 0 (control), 12, 16, and 20 months. The experiment was conducted in a completely randomized design, in a 2 × 2 × 4 factorial arrangement (conservation environment × packaging × storage period) for each species. The variables evaluated were: water content (%), germination (%), germination speed index (GSI), and mean germination time (MGT). The physiological quality of seeds of both species were preserved when seeds were maintained under controlled environment, regardless of the packaging. However, when stored under non-controlled environment, the packaging in paper bags was more efficient for the conservation of seeds of P. pachycladus subsp. pernambucoensis, and the glass container was more efficient for T. inamoena. This information may be needed for ex situ conservation of these species and to support the recovery of degraded areas susceptible to desertification in the Caatinga biome.