A Kazhdan-Lusztig variety is the intersection of a locally-closed Schubert cell with an opposite Schubert variety in a flag variety. We present a linear parametrization of the Schubert cells in the affine type A flag variety via Bott-Samelson maps, and give explicit equations that generate the Kazhdan-Lusztig ideals in these coordinates. Furthermore, our equations form a Gröbner basis for the Kazhdan-Lusztig ideals. Our result generalizes a result of Woo-Yong that gave a Gröbner basis for Kazhdan-Lusztig ideals in the type A flag variety.