Yes. As you say we may assume $D$ is very ample. So there is a closed immersion of $X$ into $\mathbb{P}^n$ such that $D$ is $X \cap H$ for some hyperplane $H$. Pick coordinates $[x_0: x_1: \ldots: x_n]$ for the ambient $\mathbb{P}^n$ such that the vanishing locus of $x_0$ is $H$. Let $f_1, \ldots, f_m$ be homogeneous equations cutting out $X$ in these coordinates. Then their dehomogenizations with respect to $x_0$ are homogeneous equations cutting out $X \setminus D$ in $\mathbb{P}^n \setminus H = \mathbb{A}^n$.