We provide insight into the vertical distribution of multi‐scale scintillation‐inducing irregularities in the low‐latitude ionosphere. In four sets of novel experiments, we sampled altitudes from 330 to 1,280 km in the 18–24 magnetic local time (MLT) sector using the Swarm Echo GPS Attitude, Positioning, and Profiling Experiment occultation receiver (GAP‐O) GPS receiver with its antenna oriented toward zenith. In order to identify multi‐scale irregularities both above and at the satellite's position, we utilize high‐sample‐rate GAP‐O amplitude and phase measurements along with a measurement of net current on the surface of the imaging and rapid‐scanning ion mass spectrometer sensor on board, which serves as a proxy for density variations. By calculating the rate of change of total electron content index using two sets of GPS parameter choices, we are able to sample irregularities as small as 160 m, which is comparable to or smaller than the Fresnel scale responsible for scintillation‐inducing irregularities. During one campaign, we find that amplitude scintillations on the GPS signal coincide with strong in‐situ small‐scale density irregularities in 32% of cases, indicative of a broad irregularity region extending from the satellite's position to hundreds of kilometers above. Also, we show that large‐scale ionospheric disturbances (larger than 80 km) occur predominantly below 500 km, and down to the 330 km perigee of Swarm Echo in the 18–21 MLT sector. In contrast, small‐scale variations of total electron content are detected at all MLTs between 18 MLT and magnetic midnight and at all altitudes sampled in this experiment. However, they are more frequent in the 22–24 MLT range. Plain Language Summary Variations in ionospheric electron density, so‐called irregularities, produce rapid fluctuations on propagating communication and navigation signals, which can be severe near the magnetic equator and in the polar regions. Due to sparse sampling, our knowledge of the vertical distribution of small‐scale irregularities is limited. The Swarm Echo satellite contains a high‐sample‐rate GPS receiver whose antenna normally points in the horizontal direction. We re‐oriented Swarm Echo for short periods to make the receiver antenna point in the vertical direction during November 2019 to November 2020 while the satellite was flying in the low‐latitude region from 18 magnetic local time (MLT) to midnight, and at altitudes between 330 and 1,280 km. This allows us to investigate the irregularity distribution at multiple scales and different altitudes. Using this novel experiment, we show that in 32% of the cases in which large density fluctuations were detected at the satellite, strong GPS scintillations were also detected, providing valuable information on their altitude distribution. We demonstrate that, between 18 and 21 MLT, ionospheric structures having large scale sizes (between 80 and 2,400 km) occur mainly below 500 km altitude, whereas total electron content variations caused by irregularities (160 m–480 km) are detected at all altitudes and throughout the 18‐midnight MLT sector. Key Points We report measurements of 50 and 100 Hz GPS carrier phase and amplitude and in situ density in the equatorial ionosphere Strong scintillations and small‐scale density irregularities are measured in situ at altitudes from 330 to 1,280 km Small scale variations of total electron content were more severe during the 22–24 magnetic local time sector