Low-dimensional quantum magnets are a versatile materials platform for studying the emergent many-body physics and collective excitations that can arise even in systems with only short-range interactions. Understanding their low-temperature structure and spin Hamiltonian is key to explaining their magnetic properties, including unconventional quantum phases, phase transitions, and excited states. We study the metal-organic coordination compound (C5H9NH3)2CuBr4 and its deuterated counterpart, which upon its discovery was identified as a candidate two-leg quantum (S=12) spin ladder in the strong-leg coupling regime. By growing large single crystals and probing them with both bulk and microscopic techniques, we deduce that two previously unknown structural phase transitions take place between 136 and 113 K. The low-temperature structure has a monoclinic unit cell that gives rise to two inequivalent spin ladders. We further confirm the absence of long-range magnetic order down to 30 mK and investigate the implications of this two-ladder structure for the magnetic properties of (C5H9NH3)2CuBr4 by analyzing our own specific-heat and susceptibility data.