A substantial number of super-Earths have been discovered, and atmospheres of transiting super-Earths have also been observed by transmission spectroscopy. Several lines of observational evidence indicate that most super-Earths do not possess massive H 2 /He atmospheres. However, accretion and retention of less massive atmospheres on super-Earths challenge planet formation theory. We consider the following three mechanisms: (i) envelope heating by pebble accretion, (ii) mass loss during giant impacts, and (iii) atmospheric loss by stellar X-ray and EUV photoevaporation. We investigate whether these mechanisms influence the amount of the atmospheres that form around super-Earths. We develop a code combining an N -body simulation of pebble-driven planetary formation and an atmospheric evolution simulation. We demonstrate that the observed orbital properties of super-Earths are well reproduced by the results of our simulations. However, (i) heating by pebble accretion ceases prior to disk dispersal, (ii) the frequency of giant impact events is too low to sculpt massive atmospheres, and (iii) many super-Earths having H 2 /He atmospheres of 10 wt% survive against stellar irradiations for 1 Gyr. Therefore, it is likely that other mechanisms such as suppression of gas accretion are required to explain less massive atmospheres ( 10 wt%) of super-Earths.