We study the ascent of granular-sized magnetic bubbles from the solar photosphere through the chromosphere into the transition region and above, for the first time. Such events occurred in a flux emerging region in NOAA 11850 on September 25, 2013. During that time, the first co-observing campaign between the Swedish 1-m Solar Telescope and the IRIS spacecraft was carried out. Simultaneous observations of the chromospheric H$alpha$ 656.28 nm and ion{Ca}{2} 854.2 nm lines, plus the photospheric ion{Fe}{1} 630.25 nm line, were made with the CRISP spectropolarimeter at the SST reaching a spatial resolution of 0.14. At the same time, IRIS was performing a four-step dense raster of the said emerging flux region, taking slit-jaw images at 133 (C~{sc ii}, transition region), 140 (ion{Si}{4}, transition region), 279.6 (ion{Mg}{2} k, core, upper chromosphere), and 283.2 nm (ion{Mg}{2} k, wing, photosphere). Spectroscopy of several lines was performed by the IRIS spectrograph in the far and near ultraviolet, of which we have used the ion{Si}{4} 140.3 and the ion{Mg}{2} k 279.6 nm lines. Coronal images from the Atmospheric Imaging Assembly of the Solar Dynamics Observatory were used to investigate the possible coronal signatures of the flux emergence events. The photospheric and chromospheric properties of small-scale emerging magnetic bubbles have been described in detail in Ortiz et al. (2014). Here we are able to follow such structures up to the transition region. We describe the properties, including temporal delays, of the observed flux emergence in all layers. We believe this may be an important mechanism of transporting energy and magnetic flux from subsurface layers to the transition region and corona.