Various phosphorus flame retardants (FR) have been grafted on lignin-rich miscanthus fibers and lignin-poor flax fibers according to two methods, phosphonic acids condensation in mild conditions and radiation grafting. Phosphorus content and its location on fibers were evaluated. Even if phosphorus FR diffused into the fibers bulk in all cases, chemical modification based on phosphonic acids condensation with hydroxyls of miscanthus fibers appears more suitable for high lignin content fibers. Phosphorus content in miscanthus fibers reached 1.4 wt% using hexane-1,6-diylbisphosphonic acid whereas it reached a lower content (0.3 wt%) for flax fibers. Radiation grafting is suitable for both fibers with limited effect depending on fiber nature. Flame retardancy at microscale was examined using PCFC and TGA. Thermal properties and flame retardancy have been shown to be correlated to the phosphorus content but also to fibers composition and to the thermal stability of the flame retardant. Vinyl phosphonic acid was found to be more efficient as char promoter for flax compared to miscanthus.