Given a hypergraph $\mathcal{H}$, the $\mathcal{H}$-bootstrap process starts with an initial set of infected vertices of $\mathcal{H}$ and, at each step, a healthy vertex $v$ becomes infected if there exists a hyperedge of $\mathcal{H}$ in which $v$ is the unique healthy vertex. We say that the set of initially infected vertices percolates if every vertex of $\mathcal{H}$ is eventually infected. We show that this process exhibits a sharp threshold when $\mathcal{H}$ is a hypergraph obtained by randomly sampling hyperedges from an approximately $d$-regular $r$-uniform hypergraph satisfying some mild degree and codegree conditions; this confirms a conjecture of Morris. As a corollary, we obtain a sharp threshold for a variant of the graph bootstrap process for strictly $2$-balanced graphs which generalises a result of Korándi, Peled and Sudakov. Our approach involves an application of the differential equations method.