Starch-guest molecule amylose inclusion complexes (AIC) are of interest to industry as a means to encapsulate and deliver compounds. Coconut fatty acids (CFA) consist predominantly of medium chain fatty acids having useful food and nonfood applications. This article describes the formation of high amylose corn (HAC)- or waxy corn starch (WC)-CFA AIC containing 0%, 2%, 7.5%, and 15% CFA using a continuous thermomechanical extrusion process at 20% feed moisture and a twin-screw extruder with a unique screw design. The extrusion conditions completely destructure both the HAC and waxy starch granules and the resulting materials are evaluated using SEM, XRD, FT-IR, FTIR-m, and TGA. The HAC-CFA materials are shown to contain AIC having 61 V type helical structure between amylose and the CFA that are confirmed by XRD and IR spectral analysis. By TGA, extruded HAC materials containing 15% CFA are shown to have excess CFA present in addition to formed AIC. In contrast, the WC is shown not to form AIC with the CFA and only trap the CFA within the starch matrix. The understanding gained from this study is helpful to design the processing of starch-based biopolymers to prepare AIC having improved functional properties for potential commercial applications.