Given $k\ge 2$ and two $k$-graphs ($k$-uniform hypergraphs) $F$ and $H$, an $F$-factor in $H$ is a set of vertex disjoint copies of $F$ that together cover the vertex set of $H$. Lenz and Mubayi were first to study the $F$-factor problems in quasi-random $k$-graphs with a minimum degree condition. Recently, Ding, Han, Sun, Wang and Zhou gave the density threshold for having all $3$-partite $3$-graphs factors in quasi-random $3$-graphs with vanishing minimum codegree condition $Ω(n)$. In this paper, we consider embedding factors when the host $k$-graph is $k$-partite and quasi-random with partite minimum codegree condition. We prove that if $p>1/2$ and $F$ is a $k$-partite $k$-graph with each part having $m$ vertices, then for $n$ large enough and $m\mid n$, any $p$-dense $k$-partite $k$-graph with each part having $n$ vertices and partite minimum codegree condition $Ω(n)$ contains an $F$-factor. We also present a construction showing that $1/2$ is best possible. Furthermore, for $1\leq \ell \leq k-2$, by constructing a sequence of $p$-dense $k$-partite $k$-graphs with partite minimum $\ell$-degree $Ω(n^{k-\ell})$ having no $K_k(m)$-factor, we show that the partite minimum codegree constraint can not be replaced by other partite minimum degree conditions. On the other hand, we prove that $n/2$ is the asymptotic partite minimum codegree threshold for having all fixed $k$-partite $k$-graph factors in sufficiently large host $k$-partite $k$-graphs even without quasi-randomness.