While indigenous organic matter has been previously reported in the Mars meteorite Nakhla, little is known as to either its form or distribution. A notable feature of Nakhla is the prevalence of secondary phases associated with aqueous alteration. By analogy with the terrestrial environment, our objective was to determine whether Martian secondary minerals could also act to accumulate and preserve such organic matter. Through a multidisciplinary approach, we have characterized the nature of carbonaceous matter and spatially associated phases within the Martian meteorite Nakhla using a wide-ranging suite of analytical instrumentation including optical microscopy, laser Raman spectroscopy, focused ion beam microscopy, secondary ion mass spectrometry, and scanning and transmission electron microscopy. In freshly fractured chips of Nakhla, we found carbonaceous phases intimately associated with secondary aqueous alteration phases, both mineral and amorphous, interpreted to have formed through the low-temperature aqueous dissolution of the host basalt while on Mars. The carbonaceous matter is present both in condensed phases and in a dispersed state spatially associated with secondary alteration phases. In the former, we identified discrete refractory micron to submicron assemblages that appear macromolecular in nature and, in several cases, associated with fluorine and, in one case, significant nitrogen. Textural, chemical, mineralogical and isotopic considerations argue for a non-terrestrial origin of this carbonaceous matter. Additionally, we report the presence of the ferrous hydroxycarbonate mineral chukanovite (Fe2OH2CO3) within some of the secondary mineral aggregates studied. Neither the intimate association of carbonaceous matter with secondary phases nor the identification of chukanovite have been previously reported in any of the Martian meteorites. In this regard, we note such microscale features within alteration phases would most likely be lost in the preparation of conventional polished thin sections and thus explain why they have not been previously reported. In lieu of sample return, the sui generis nature provided by Mars meteorites provide insight to alteration processes on Mars currently denied to robotic exploration and remote sensing. Our results show a variety of habitability-related sample attributes, formed hundreds of millions of years ago near Mars’ surface, have persisted there until very recently and may be more widespread in the surface regolith than previously thought. This may have implications in sample selection criteria for Mars sample return.