Precise adherence to the manufacturer’s instructions and requirements plays an important role in various installation processes. The presented paper deals with the evaluation of the effect of manufacturing imperfections and surface defects on the failure behaviour of flexible adhesive intended for façade application. The failure to comply with the accepted procedures is more common in construction practice than in other sectors of the industry, mostly due to the surrounding conditions and lack of trained supervision. Unfortunately, this may lead to premature failure of adhesively bonded joints and a considerable shortening of the service life of the entire construction. To determine the potential of the risk, five types of artificially applied (a) manufacturing imperfections: (1) application on wet adhesion promoter, (2) application after the expiry of the laying-time, (3) curing of samples at +1℃ (b) surface defects: (4) application on a wet substrate and (5) application on a dirty surface, were suggested. Moreover, the Taguchi L32 orthogonal array design was used to arrange the test setup of all possible combinations. The 1 K polyurethane adhesive was applied in tensile butt joints and single-lap shear joints composed of aluminium alloy and thermally modified wood substrates. The obtained results confirmed that non-observance of the required manufacturing techniques and recommended procedures can have a negative impact on the decrease of the adhesively bonded joint strength and deformation behaviour. Surprisingly, the most critical was not the combination of all suggested types of imperfections and defects. The performed one-way ANOVA revealed that the most perilous was the combination of types 2 and 4 in the tensile test with 77% joint strength reduction. In the shear test, the most critical was the combination of all types of imperfection and defects which led also to a 77% drop of shear strength.