The purpose of the paper is to provide practical information on the selection of heat treatment conditions and the prevention of secondary microbial contamination of liquid sugar. The guidelines included in the paper were formulated on the basis of practical experience gained. The most important aspect often refers to the unnoticed cause of secondary contamination of liquid sugar after heat treatment, during its cooling in diaphragm heat exchangers along with the indication of the possibility of elimination of this cause. The article also presents the results of microbiological analysis in the field of heat resistance of microorganisms present in raw juice, obtained from the extractor. The data indicate the difficulty of thermal inactivation of mesophilic and thermophilic spores present in the studied environment. The cited results of microbiological analysis prove the usefulness of the measures to prevent secondary microbial contamination of the finished product.