Corn starch is frequently used as a thickening agent in food products because of its stability under thermal processing conditions. However, with fluctuating raw material costs due to weather conditions, disruptions in supply chains, and geopolitical challenges, there is an increasing need to explore alternative sources of starch. This study examines the effect of retort processing on the heat penetration and physicochemical aspects of modified corn, tapioca, and potato starches in Alfredo sauce. Modified corn starch, commonly used in commercial sauces, was compared with tapioca and potato starches to evaluate their effects on viscosity, color, and processing times required to achieve a F0 = 6 for Clostridium botulinum. Using the reference starch concentration of 1.90%, modified corn starch showed a significant increase in viscosity from 3,328 cP to 13,296 cP with a processing time of 31.33 min. Modified tapioca starch, at the same concentration, increased from 3440 cP to 8176 cP over 38.38 min, indicating superior thermal stability being the longest cooking time evaluated between all samples. For modified potato starch, using the reference concentration, viscosity increased from 1,200 cP to 4,656 cP, with a processing time of 31.93 min. Adjusting the starch concentration to 3% for modified tapioca starch and 2.38% for modified potato starch increased viscosity to 14,400 cP and 16,336 cP, respectively. These adjustments resulted in a darker Alfredo sauce, with the L value decreasing from 92.27 to 83.67 due to the longer cooking time. Heat penetration findings suggest that modified potato starch can replace modified corn starch safely using the reference concentration (1.90%) without altering the process holding time but requiring further adjustments to match commercial viscosity standards, while modified tapioca starch, although requiring higher concentrations and longer processing times, was tested for retention time at 3.00% and to be a feasible alternative. This study offers valuable insights to the food industry in selecting appropriate starches to maintain the quality and safety of thermally processed Alfredo sauce.