We have used Spitzer and its IRAC camera to search for the transit of the super-Earth HD 40307b. The transiting nature of the planet could not be firmly discarded from our first photometric monitoring of a transit window because of the uncertainty coming from the modeling of the photometric baseline. To obtain a firm result, two more transit windows were observed and a global Bayesian analysis of the three IRAC time series and the HARPS radial velocities was performed. Unfortunately, any transit of the planet during the observed phase window is firmly discarded, while the probability that the planet transits but that the eclipse was missed by our observations is nearly negligible (0.26%).