For a countable admissible ordinal $\alpha$, let $\mathcal{L}_\alpha=\mathcal{L}_{\infty,\omega}\cap L_\alpha$ and let $\equiv_\alpha$ be the corresponding elementary equivalence relation. Say that such an $\alpha$ is locally Fraissean iff there is an $\mathcal{L}_\alpha$-sentence $\eta$ in the language $\{R,S,A,B\}$, with $R,S$ binary relation symbols and $A,B$ unary relation symbols, such that for every pair of $\{R\}$-structures $\mathcal{X},\mathcal{Y}\in L_\alpha$ we have $$\mathcal{X}\equiv_\alpha\mathcal{Y}\quad\iff\quad\exists\mathcal{M}\in L_\alpha[\mathcal{M}\models\eta\wedge (A^\mathcal{M}\cong\mathcal{X}\wedge B^\mathcal{M}\cong\mathcal{Y})^{L_\alpha}]$$ (the $L_\alpha$-superscript meaning that relevant isomorphisms have to exist within $L_\alpha$ itself).
For example, if $\equiv_\alpha$ coincides with $\cong$ on $\{R\}$-structures in $L_\alpha$, then $\alpha$ is locally Fraissean; in particular, if $L_\alpha\equiv L_{\omega_1}$ then $\alpha$ is locally Fraissean. But this seems like overkill:
What is the smallest locally Fraissean ordinal?
It's already not clear to me whether $\omega_1^{CK}$ is locally Fraissean - in particular, the argument Farmer S. gave that $\mathcal{L}_{\omega_1,\omega}$ doesn't satisfy the "global" version of the property above doesn't seem to trivially effectivize (although I could be missing something).