A bit of background ... I have a degree in Food, Nutrition and Health Science and a Masters in Clinical Nutrition. I currently work in molecular biology after 2 years in the biophysical lab in the same company. My new boss has offered to pay for training or further education for me. At the moment I work with a novel technology as a replacement for antibodies, and the research I am doing, I think, would be a good topic for a PhD as its all new information I am gathering. Is there a way for me to use my work at work as a PhD? Would a uni let me do my work here and still give me a qualification for it?

There's no reason why not, as long as there aren't unusually strict NDAs that make it impossible to publish results. If it's good theoretically-solid research it shouldn't matter whether it's being carried out as part of some professional work or not (in fact some disciplines would see that as a plus in terms of guaranteed industrial relevance)

The main danger I would concern myself with would be juggling the need for rapid progress associated with your professional stakeholders with the need for sufficient procedural rigour for academic credibility. I don't know your domain well at all though, so maybe that's not as much of an issue as other areas.