support low-energy excitations. These defects can take a wide variety of microscopic forms, and for amorphous materials are broadly described using generic models such as the tunneling two-level systems (TLS) model. Although the details of TLS, and their impact on the low-temperature behavior of materials have been studied since the 1970s, these states have recently taken on further relevance in the field of quantum computing, where the limits to the coherence of superconducting microwave quantum circuits are dominated by TLS. Efforts to mitigate the impact of TLS have thus far focused on circuit design, material selection, and material surface treatment. In this work, we take a new approach that seeks to directly modify the properties of TLS through nanoscale-engineering. This is achieved by periodically structuring the host material, forming an acoustic bandgap that suppresses all microwave-frequency phonons in a GHz-wide frequency band around the operating frequency of a transmon qubit superconducting quantum circuit. For embedded TLS that are strongly coupled to the electric qubit, we measure a pronounced increase in relaxation time by two orders of magnitude when the TLS transition frequency lies within the acoustic bandgap, with the longest T1 time exceeding 5 milliseconds. Our work paves the way for in-depth investigation and coherent control of TLS, which is essential for deepening our understanding of noise in amorphous materials and advancing solid-state quantum devices.