To evaluate the remineralising effects of fluoride (F) varnishes containing bioavailable calcium-phosphate compound (Ca-P) based remineralisation systems and 5000 ppm F toothpaste (FTP) on root caries lesions (RCLs) and the potential effects of proanthocyanidin (PA) for the treatments of RCLs when used as an adjunct to F regimens. Demineralised root dentine and a pH-cycling model were used to mimic RCLs and the oral environment. Remineralising effects of MI VarnishTM (MIV) containing casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) and Clinpro™ White Varnish (CPWV) containing tri-calcium phosphate (TCP) along with FTP and PA were evaluated regarding the birefringence, elemental composition, mechanical properties and mineral density of remineralised dentine with DuraphatTM as a comparison. MIV, CPWV and DuraphatTM promoted the incorporation of F into RCLs and increased mineral density but did not change microhardness of root dentine significantly. Surface microhardness increased significantly when MIV or CPWV was used with 5000 ppm FTP. Application of PA with F regimens significantly increased subsurface mineral density. When PA was applied with MIV or CPWV along with FTP, the highest ion uptake and relative mineral gain (%ΔZ) was achieved, and significant increase of microhardness was up to 30 μm depth. Generally, MIV was associated with a higher mineral content gain than CPWV. Treatment of carious root surfaces remains challenging due to the complex pathological processes and difficulty in restoring the highly organised structure of root dentine. Treatment strategies targeting both remineralisation and preservation of the dentinal organic matrix have the potential to improve the fluoride-mediated remineralisation approaches.