Word for earning less than spent

A common expression for this would be (operating) at a loss:

Making less money than is spent buying, operating, or producing something. ‘a railway running at a loss’
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I would say that the company has been in the red:

The expression "in the red" generally is used to describe a business that is operating at a loss.
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This expression can also be applied to individuals, but it is most often used with businesses.

Another option is simply in debt.

For people, you could say they are "living beyond their means". According to Collins English Dictionary

If someone is living beyond their means, they are spending more money than they can afford.

This isn’t used so much for companies, but you could say they are "making a loss".