Research on the neural basis of conscious perception has almost exclusively shown that becoming aware of a stimulus leads to increased neural responses. By designing a novel form of perceptual filling-in (PFI) overlaid with a dynamic texture display, we frequency-tagged multiple disappearing targets as well as their surroundings. We show that in a PFI paradigm, the disappearance of a stimulus and subjective invisibility is associated with increases in neural activity, as measured with steady-state visually evoked potentials (SSVEPs), in electroencephalography (EEG). We also find that this increase correlates with alpha-band activity, a well-established neural measure of attention. These findings cast doubt on the direct relationship previously reported between the strength of neural activity and conscious perception, at least when measured with current tools, such as the SSVEP. Instead, we conclude that SSVEP strength more closely measures changes in attention.