Apatite and rare earth elements (REEs) are vital to the European Union’s economic growth and resource security, given their essential roles in fertilizers, green technologies, and high-tech applications. To meet rising demand and reduce reliance on imports, the exploitation of domestic deposits has become increasingly important. This study investigates the beneficiation potential of ore from a carbonatite complex (Finland), focusing on the recovery of fluorapatite concentrate through froth flotation. This research addresses two key objectives: evaluating the potential for REE enrichment alongside fluorapatite concentration using conventional anionic and amine-based reagents, and assessing separation efficiency when partially substituting the most effective conventional collectors with bio-based organosolv lignin nanoparticles. Adequate recovery rates for apatite and REEs were achieved using common anionic collectors, such as hydroxamate and sarcosine, yielding P grades of 23.4% and 21.5%, and recoveries of 96.4% and 89.2%, respectively. Importantly, concentrate quality remained stable with up to a 30% reduction in conventional collectors and the addition of organosolv lignin. Bench-scale trials further validated the approach, demonstrating that lanthanum and cerium recoveries exceeded 71%, alongside satisfactory apatite recovery. Lignin nanoparticles were observed to interact with both minerals; however, the interaction was more pronounced in the case of phlogopite, which exhibited a markedly greater increase in surface hydrophilicity following treatment, suggesting a stronger affinity or surface modification effect, which was beneficial to the performance of the separation process.