No, see Example 6.1 in Tam's and Schneider's paper On the Core of a Cone-Preserving Map. For completeness, I will write the counterexample here, but the details can be found in the paper.
Let $V = \mathbb{R}^3$ and consider the cone $C = \{(x,y,z) \in \mathbb{R}^3 \mid 2xz - y^2 \geq 0 \text{ and } x \geq 0 \}$. Then for
$$
A =
\begin{bmatrix}
1 & 1 & 1/2 \\
0 & 1 & 1 \\
0 & 0 & 1
\end{bmatrix},
$$
we have $AC = C$, but $A$ is not diagonalizable over $\mathbb{C}$. It is true, however, that any automorphism of a cone which has an eigenvector in the interior of the cone is diagonalizable over $\mathbb{C}$. In this case, the condition does not hold as the only eigenvector lies on the boundary.
References
Tam, Bit-Shun; Schneider, Hans, On the core of a cone-preserving map, Trans. Am. Math. Soc. 343, No. 2, 479-524 (1994). ZBL0826.15015.