This study presents the quality control of the conservation treatment (deacidification with calcium hydroxide solution) applied to the paper of the Historical Archives of KKE (Greek Communist Party) after the flood of 1994. Fundamental chemical, mechanical and optical properties of paper were examined (pH, folding endurance and the colour coordinates L* and b* of the CIE L*a*b* system), along with structural properties by fiber optics microscopy. The decrease of the deterioration rate of these properties of paper is one of the aims of conservation. The results showed deceleration of the deterioration of the measured properties due to the conservation treatment after 6 days of accelerated ageing at 105°C. Only the optical properties of the samples containing lignin degraded as a result of lignin oxidation in the highly alkaline environment of the deacidification bath. The principal component analysis revealed a strong relation between the colour coordinates and the mechanical strength of the samples without a lignin component. It is believed that the experimental procedure followed in this study can be utilized for routine quality control of the conservation treatments in a well-organized archival institution.