Maca (Lepidium meyenii) is a high-Andean crop whose subterranean storage organs (hypocotyls) show distinctive colors that are related to pharmacological properties. Little is known about seed color variation and its influence on germination performance, hypocotyl pigmentation and plant survival. Germination rate is critical for maca plants to survive frost events during early development. We evaluated the effect of germination promoters (gibberellic acid and sodium hypochlorite) and temperature regimes (constant and cold: 4°C; variable and moderate: 5–10°C; constant and warm: 16°C) on germination of seeds with different embryo color (yellow, reddish-purple and blue). We also assessed the association between seed color, hypocotyl color and plant survival under field conditions. Seeds with blue and yellow embryos had the lowest and highest germination rates, respectively, across cold and moderate temperature regimes. At warm temperature, germination was not affected by seed color. Germination promoters only enhanced seed germination at cold and moderate temperatures. In the field, black seeds (with blue embryos) showed the greatest survival. Seeds with reddish-purple embryos produced a higher proportion of pigmented hypocotyls–mainly purple–than other seed colors. Seed color should be taken into account in maca breeding programs, particularly in the context of climate change.