The company has been in the red for the last 2 years.
He has been working in the red for the last few months.
phrase ~ If a person or company is in the red or if their bank account is in the red, they have spent more money than they have in their account and therefore they owe money to the bank. from Collins Dictionary
This commonly used idiom is based on the historically traditional book-keeping practice of using red ink for outstanding balances in ledgers. From what I gather, the practice was rather informal or optional (depending on company or individual preferences), although often used by old-fashioned book-keepers who entered all information into their ledgers by hand. Many of them kept pens of different colored inks, each of which had a specific symbolic meaning. Red ink could mean almost anything, depending on how it was implemented, but relevant to this particular popular idiom, it meantmoney owed.
A less common word that might apply is impecunious. The strict definition means someone (or an entity) with no money or assets, but I've often heard it used to mean someone who is not good at managing their money.
For an individual, a common way of saying it is, "living beyond his means". Depending on how formal the language of the document is, for a company you could say, "spending beyond its means" or "spending beyond their means".