(1) Background: According to the IUCN, Boswellia pirottae is classified as a vulnerable species. However, knowledge of its seed characteristics and germination behaviour is lacking. (2) Methods: The aim of this research was to characterise the seeds and evaluate the effects of seed colour and controlled temperatures on seed germination. The seeds were segregated into the following colour categories: light brown (LB), brown (B), and dark brown (DB). The seeds were evaluated under controlled constant temperatures (23 °C) and at room (fluctuating) temperature independently. One-way ANOVA, t-test, and germination indexes were used for analyses. (3) Results: The results showed significant differences in the mean seed masses of LB, B, and DB seeds. Similarly, the differently coloured seeds varied in their water imbibition rates. The result showed significant differences in the mean germination of the seeds in both the controlled temperature (23 °C) and room-temperature chambers among the LB, B, and DB seeds. However, the t-test revealed no significant differences in the mean germination of the seeds of similar colours between controlled temperature and room temperature conditions. (4) Conclusions: The seed’s colour significantly influenced the seed mass, water imbibition capacity, and germination rate relative to the temperature treatment. Dark brown seeds are recommended for seed collection aimed at seedling propagation.