Jerusalem artichoke (JA) tubers are rich in minerals, fibers and inulin, a unique polysaccharide stored in them instead of starch. In this study, JA tubers were dried and ground into flour, which was then used to substitute 2.5, 5, 7.5 and 10% of wheat flour to prepare functional cookies using the previously mentioned functionality (minerals and fibers). The chemical composition of cookies was investigated, as well as the effects of substituting wheat flour for JA tubers flour (JAF) on it. JAF increased the moisture content of cookies, resulting in increased hardness and fractur ability. Fiber content increased as well, reaching a maximum of 0.8% at the highest substitution rate (10%). Ash content was increased from 0.6 to 1.09%, which was also related to the increased minerals (magnesium, calcium, phosphorus and iron), giving the prepared cookies high nutritional values. Physical properties of cookies including spread ratio, specific volume, and color showed marginal changes due to higher fiber and moisture contents in the prepared cookies. Furthermore, the sensory characteristics of JA cookies yielded satisfactory results, as overall acceptability was not significantly affected, although color was altered because of the pale or dark colored cookies at higher levels of substitution.