We describe a broadly applicable experimental proposal to search for the violation of local Lorentz invariance (LLI) with atomic systems. The new scheme uses dynamic decoupling and can be implemented in current atomic clock experiments, with both single ions and arrays of neutral atoms. Moreover, the scheme can be performed on systems with no optical transitions, and therefore it is also applicable to highly charged ions which exhibit a particularly high sensitivity to Lorentz invariance violation. We show the results of an experiment measuring the expected signal of this proposal using a two-ion crystal of Sr-88(+) ions. We also carry out a systematic study of the sensitivity of highly charged ions to LLI to identify the best candidates for the LLI tests.