Potato has great nutritional and economic importance in agriculture. However, Rhizoctonia solani represents a significant risk, reducing the yield and quality of potato production. Flesh-colored potato (FCP) extracts show in vitro inhibitory effects against R. solani, although environmental factors may reduce their stability. Solid lipid nanoparticles (SNLs) offer a solution by encapsulating these compounds, preventing degradation, and improving delivery, positioning solid lipid nanoparticles as a promising technology for sustainable extract application. A greenhouse potato assay at two phenological stages under R. solani inoculation was used to evaluate the photosynthetic response (photosynthetic parameters and pigments) to two doses of the nanoencapsulated extract (SNL + FCP). During inoculation and commercial fungicide application, stomatal conductance, the photosynthetic rate, and the internal CO2 concentration increased compared with those of the non-inoculated control (NT), whereas the nanoencapsulated extract maintained levels similar to those of the NT, suggesting the possible regulation of the photosynthetic defense system. In terms of photosynthetic pigments, SLN + FCP maintained chlorophyll concentrations, unlike those in inoculated plants, which significantly decreased. Component analysis revealed that a lower dose primarily increased chlorophyll B synthesis, whereas a higher dose increased chlorophyll A compared with the inoculated control. These findings suggest an improved response from SLN + FCP to commercial fungicides, particularly with respect to photosynthetic pigments. However, further research is needed, and the results indicate promising potential for the eco-friendly control of phytopathogenic fungi in agriculture.