The shear strength of furfurylated, N-methylol melamine (NMM) and thermally modified wood bonded with emulsion polymer isocyanate, polyvinyl acetate (PVAc), and polyurethane (PU) adhesives was examined. Furfurylation and NMM modification of Scots pine had a significant negative effect on the bonding strength with all adhesives irrespective of the treatment intensity. The obtained low-shear strength values were related to the brittle nature of the wood after modifications rather to the failure of the bondline. PVAc showed a better bonding performance with both furfurylated and NMM modified wood while the combination of furfurylated wood and PU gave the highest reduction in bonding strength (47–51%). Shear strength also decreased significantly after thermal modification in both Scots pine (36–56%) and beech (34–48%) with all adhesives. With the exception of thermally modified beech samples bonded with PU, bondline was found to be the weakest link in thermally modified wood as it was revealed by the wood failure surfaces. Bondline thickness and effective penetration of adhesives did not relate to the shear strength of all modified wood materials. The lower shear strength of modified wood could be attributed to other factors, such as the reduced chemical bonding or mechanical interlocking of adhesives, and the reduced strength of brittle modified wood substrate.