We investigate the problem of deciding first-order theories of finite trees with several distinguished congruence relations, each of them given by some equational axioms. We give an automata-based solution for the case where the different equational axiom systems are linear and variable-disjoint (this includes the case where all axioms are ground), and where the logic does not permit to express tree relations x=f(y,z). We show that the problem is undecidable when these restrictions are relaxed. As motivation and application, we show how to translate the model-checking problem of Apil, a spatial equational logic for the applied pi-calculus, to the validity of first-order formulas in term algebras with multiple congruence relations.