Abstract: The objective of this study was to determine the effect of six types of flours, namely corn flour, rice flour, glutinous rice flour, soy flour, cassava flour and oat flour. These flours were used to replace Whole Milk Powder (WMP) at 20, 15, 15, 15, 10 and 5%, respectively. Goat Milk Yoghurt (GMY, 18% total solid) fortified with flour was compared to control group (non fortified flour) in microstructure. Microstructure was determined by Transmission Electron Microscopy (TEM). The results showed that all flours can prevent whey separation and improve texture of GMY as compared to control group. TEM micrographs demonstrated that the microstructure of GMY gel with all the flours were more firm than the control group and showed the interaction of flour with casein micelles and their participation in the formation of the gel structures. It exhibited protein network (casein micelle chain), fat globules and bacteria in all samples and showed that flour types have an influence upon the association of casein micelles and thus affect microstructure.