SummaryThis objective of this study was to determine the effect of protein‐ and carbohydrate‐based fat replacers on the microstructure of low‐fat Cheddar cheese. Microstructure was studied by transmission and scanning electron microscopy. Protein‐based fat replacers were Dairy Lo™ (DL) and Simplesse™ (SIMP), while the carbohydrate‐based fat replacers were Novagel™ (NOV) and Stellar™ (STEL). Low‐fat Cheddar cheese was manufactured using these commercial fat replacers and aged for 6 months at 5 °C. Low‐fat control (LFC) and low‐fat Cheddar cheese made with SIMP and DL showed a rippled surface microstructure while incorporation of NOV and STEL resulted in cheese with an undulated and rough surface microstructure. Cheese made with SIMP showed void areas around the SIMP particles. Fat replacers SIMP and NOV softened low‐fat Cheddar cheese by imparting discontinuity to the casein matrix. A method in which fat replacers DL and STEL appeared to soften low‐fat Cheddar cheese was by having the fewest layers (that conceivably resist crushing) at the fat–protein interface. Microstructure of low‐fat Cheddar cheese was effected by fat replacers.