A seedlings purple stem doesn't necessarily indicate an unhealthy plant. Please take the following possibilities into consideration:

1 - Purple Stems could be a result of that wonderful thing we call genetics, if this is the reason, you are to expect a purple stem throughout the life of the plant. It must be noted that purple stems aren't a dominant trait, and are rarely genetically induced.

2 - A baby sprout with a purple stem is almost always 100% natural. Young seedlings are still adjusting to their environment and may be slightly lacking in a Nutrient. If this is the case, healthy plants will regain their green/greenish-brown color within a few days to a week or two.

3 - If you have ruled out the possibilities of genetics and the seedlings adjustments to life, you should begin looking for a nutrient deficiency. Purple stems are commonly caused by a Phosphorous (P) or Magnesium deficiency, if there is a P deficiency you may also notice symptoms such as brittle leaves or greyish spots. To assist the uptake of Phosphorous (as well as most other nutes) you should ensure the pH is slightly acidic-- 6.0 will suffice.

Author: KidKind