We have systematically investigated the effect of annealing on the superconductivity of the iron chalcogenide Fe1+y(Te1−xSex). The atmospheres used for annealing include O2, N2, I2 vapor, air and vacuum. We observed that annealing in O2, I2 and air could enhance the superconductivity of underdoped samples, consistent with the results reported in the literature. Interestingly, we found that annealing in N2 also leads to a superconductivity enhancement, similar to the annealing effects of O2, I2 and air. However, vacuum annealing does not enhance the superconductivity, which indicates that the enhanced superconductivity in O2-, N2- , I2- and air-annealed samples is not due to improved homogeneity. In addition, we treated underdoped samples with nitric acid, which is found to enhance the superconductivity as well. Our analyses of these results support the argument that the superconductivity enhancement, caused either by annealing or nitric acid treatment, originates from the variation of interstitial Fe. The interstitial Fe, which is destructive to superconducting pairing, can be reduced by annealing in oxidation agents or nitric acid treatment. We also find that although N2-, O2- and air-annealed samples exhibit strong superconducting diamagnetism with −4πχ ∼ 1 (χ, dc magnetic susceptibility) for some samples, their actual superconducting volume fraction probed by specific heat is low, ranging from 10% to 30% for 0.09 < x < 0.3, indicating that the superconductivity suppression remains significant even in annealed samples. The strong diamagnetism is associated with the superconducting shielding effect on the non-superconducting phase. We have also established the phase diagram of the annealed samples and compared it with that of the as-grown samples. The effect of annealing on the interplay between magnetism and superconductivity is discussed.