Let $X = V(I) = Spec(\mathbb{Z}[x_1,\dots,x_n]/I)$ with $I=(f_1,\dots,f_m)$. The starting point is that $X(\mathbb{C})$ is finite. This implies that $X_\mathbb{C}$ is zero-dimensional, thus so is $X_\mathbb{Q}$, so it is discrete.
The question Closed points are dense in $\operatorname{Spec} A$ recalls why closed points are dense, which is a consequence of the Nullstellensatz. But since $X_\mathbb{Q}$ is a discrete space, it means that all points are closed.
Now a closed point is always defined over a finite extension, so in particular it is defined over $\overline{\mathbb{Q}}$.
I will break down this reasoning in a proof as elementary as possible. In particular, I make use of the analytical topology of $\mathbb{C}^n$ to simplify an argument.
Let $A = \mathbb{Q}[x_1,\cdots,x_n]/I$, and $V(K) = \{ a\in K^n\,|\ \forall i,\, f_i(a)=0\}$ for all fields $K$ of characteristic $0$. Then there is a canonical bijection between $V$ and the ring morphisms $A\to K$ : each $\varphi: A\to K$ defines $(\varphi(x_1),\dots,\varphi(x_n))\in V(K)$, and for each $a\in V$ there is a unique $\varphi:A\to K$ such that $\varphi(x_i)=a_i$.
Our starting point is that $V(\mathbb{C})$ is finite, and we want $V(\mathbb{C}) = V(\overline{\mathbb{Q}})$
First we show that every prime ideal of $A$ is maximal. Indeed, suppose we have $\mathfrak{p}\subset A$ prime but not maximal. Then there is $\mathfrak{q}\subset \mathbb{Q}[x_1,\dots,x_n]$ prime but not maximal with $I\subset \mathfrak{q}$ (according to the description of the prime ideals of a quotient ring). Now the irreducible variety in $\mathbb{C}^n$ it defines must be pathwise connected so it is infinite and for each $a$ in this variety you have $\mathfrak{q}\subset \mathfrak{m}_a\subset \mathbb{C}[x_1,\dots,x_n]$. In particular each of these $\mathfrak{m}_a$ contains $I$ and this each of these $a\in \mathbb{C}^n$ are actually in $V(\mathbb{C})$, which is a contradiction.
Now let $a\in V(\mathbb{C})$, and let $\varphi: A\to \mathbb{C}$ be the corresponding morphism. Then $\varphi(A)\subset \mathbb{C}$ so $\varphi(A)$ is an integral domain, and in particular $\mathfrak{p}= \ker(\varphi)$ is prime. Then it must be maximal, so $\varphi(A) = A/\mathfrak{p}$ is a finitely generated algebra over $\mathbb{Q}$ which is a field, so by Zariski's lemma, it is a finite extension of $\mathbb{Q}$. Hence $\varphi(A)\subset \overline{\mathbb{Q}}$, so $a\in V(\overline{\mathbb{Q}})$.
If you want the $f_i$ to have coefficients in $\overline{\mathbb{Q}}$ you can just replace $\mathbb{Q}$ by $\overline{\mathbb{Q}}$ everywhere in the proof.