The expression of codon optimised genes is a popular genetic engineering approach for the production of industrially relevant proteins. This study investigates and compares the expression of codon optimised and codon adapted amylase variants. The Aspergillus tubingensis raw starch hydrolysing α-amylase (amyA) and glucoamylase (glaA) encoding genes were redesigned using synonymous codons and expressed in Saccharomyces cerevisiae Y294. Codon optimisation to favour S. cerevisiae codon bias resulted in a decrease in extracellular enzyme activity of 72% (30.28 nkat ml-1) and 68% (4.08 nkat ml-1) compared to the expression of the native amyA and glaA genes, respectively, after 96 h of growth. However, a lower cultivation temperature and co-expression with the PDI1 gene increased extracellular activity levels of the codon optimised α-amylase and glucoamylase, respectively. Despite the identical amino acid sequence of GlaA, GlaA_Opt and GlaA_CBI, differential scanning fluorimetry revealed changes in the glucoamylase proteins' melting temperatures (>3°C). Shifts in the fluorescence curves suggest changes in glucoamylase tertiary structure. Results indicate that synonymous codon changes resulting from codon optimisation of amyA and glaA genes does not guarantee increased recombinant protein production and that there is crucial translational information present within the coding sequence that controls protein folding and secretion.