We show that for $β\ge 1$ the semigroups of $β$-Laguerre and $β$-Jacobi processes of different dimensions are intertwined in analogy to a similar result for $β$-Dyson Brownian motion recently obtained by Ramanan and Shkolnikov. These intertwining relations generalize to arbitrary $β\ge 1$ the ones obtained for $β=2$ by the author, O'Connell and Warren between $h$-transformed Karlin-McGregor semigroups. Moreover they form the key step towards constructing a multilevel process in a Gelfand-Tsetlin pattern leaving certain Gibbs measures invariant. Finally as a by product we obtain a relation between general $β$-Jacobi ensembles of different dimensions.