Aims: We set out to study the use of cross-correlation techniques to infer the frequency shifts that are induced by changing magnetic fields in p-mode frequencies and to provide a precise estimation of error bars. Methods: This technique and the calculation of the associated errors is first tested and validated on the Sun where p-mode magnetic behaviour is very well known. These validation tests are performed on 6000-day time series of Sun-as-a-star observations delivered by the SoHO spacecraft. Errors of the frequency shifts are quantified through Monte Carlo simulations. The same methodology is then applied to three solar-like oscillating stars: HD 49933, observed by CoRoT, as well as KIC 3733735 and KIC 7940546, observed by Kepler. Results: We first demonstrate the reliability of the error bars computed with the Monte Carlo simulations using the Sun. From the three stars analyzed, we confirm the presence of a magnetic activity cycle in HD 49933 with this methodology and we unveil the seismic signature of ongoing magnetic variations in KIC 3733735. Finally, the third star, KIC 7940546, seems to be in a quiet regime.