Yes, as long as you (a) keep the organic product physically separate from the non-organic product, and document that separation, and (b) assure that your equipment is cleaned such that the organic product won't be contaminated by non-organic residues or substances (e.g. cleaning fluids) prohibited under organic certification.
Typically a plant designates a specific time of day or day of the week to do all the organic processing at once. Often organic is the first run of the day, after a complete clean-up and clean-out.
