diff --git a/lammps/src/COLVARS/colvarproxy_lammps.cpp b/lammps/src/COLVARS/colvarproxy_lammps.cpp
index b305a615f..50a413be4 100644
--- a/lammps/src/COLVARS/colvarproxy_lammps.cpp
+++ b/lammps/src/COLVARS/colvarproxy_lammps.cpp
@@ -66,13 +66,6 @@ void colvarproxy_lammps::init()
   boltzmann_ = _lmp->force->boltz;
   set_integration_timestep(_lmp->update->dt * _lmp->force->femtosecond);
 
-  if (_lmp->update->ntimestep != 0) {
-    cvm::log("Setting initial step number from LAMMPS: "+
-             cvm::to_str(_lmp->update->ntimestep)+"\n");
-    colvarmodule::it = colvarmodule::it_restart =
-      static_cast<cvm::step_number>(_lmp->update->ntimestep);
-  }
-
   if (cvm::debug()) {
     cvm::log("atoms_ids = "+cvm::to_str(atoms_ids)+"\n");
     cvm::log("atoms_refcount = "+cvm::to_str(atoms_refcount)+"\n");
@@ -111,17 +104,25 @@ void colvarproxy_lammps::set_replicas_communicator(MPI_Comm root2root)
 }
 
 
-// re-initialize data where needed
+// Initialize Colvars now that LAMMPS data structures are set up
 int colvarproxy_lammps::setup()
 {
   int error_code = colvarproxy::setup();
   set_integration_timestep(_lmp->update->dt * _lmp->force->femtosecond);
+  if ((_lmp->update->ntimestep != 0) && (colvars->it == 0)) {
+    // Note: initializing here and not in the constructor so that the Colvars
+    // configuration can be first read when the internal step is still zero
+    cvm::log("Setting initial step number from LAMMPS: "+
+             cvm::to_str(_lmp->update->ntimestep)+"\n");
+    colvars->it = colvars->it_restart = static_cast<cvm::step_number>(_lmp->update->ntimestep);
+  }
   error_code |= colvars->update_engine_parameters();
   error_code |= colvars->setup_input();
   error_code |= colvars->setup_output();
   return error_code;
 }
 
+
 // trigger colvars computation
 double colvarproxy_lammps::compute()
 {