There's actually a grammatical problem here. I'm assuming you want to describe a company that has a low profit. Your intention is to link lowly and profitable to produce the idea that the company is making almost no profit at all.
The idea is perfectly fine. There's nothing wrong about referring to a word and then qualifying it with contrasting words. ("They had a chaotic plan." "It was an almost tasteless flavour.")
However, the word you have chosen, lowly, is a tricky English word. It looks like an adverb with the -ly ending, but it's actually an adjective with a fairly specific meaning. It means low born, humble, ordinary, as in these examples from Collins:
- He was a man of lowly birth, unlike the princess.
- He was just a lowly photographer.
So what words would be better? You could say:
- a barely profitable company
- a company that was only just profitable.
- a company that made very little profit.
- a minimally profitable company