Mass spectrometry imaging (MSI) collects mass spectra of organic compounds from individual micrometer-sized spots and yields high-resolution images of the spatial distribution of target analytes on sample surfaces. MSI can potentially open a new avenue to ultra-high resolution molecular stratigraphy by resolving the fine-scale distribution of molecular biomarkers in geological records. However, ionization of organic molecules within their sediment matrix remains a critical challenge. Building on the recent introduction of MSI of archaeal tetraether lipids, we have extended the analytical spectrum to additional biomarkers and provide guidelines for the generation of multiproxy, ultra-high resolution paleoenvironmental records. We evaluated the addition of artificial matrices to promote ionization, defined the most suitable MS settings, and increased analytical complexity from pure compounds to their investigation in sediment. Most compounds relevant to molecular stratigraphy are not properly ionized in the presence of conventional matrices, but require atypical ones, such as those based on carbon or silver. Sediments serve as a natural matrix, directly allowing detection of many of these compounds. However, the sediment matrix also inhibits some reactions that otherwise promote detection, such as derivatization of alkenones or silver-mediated ionization of n-alkanes. The robustness of MSI-based molecular stratigraphy is enhanced by analysis of target compounds in narrow m/z ranges, and by summation of mass spectra from several coeval measurement spots. We present an initial inventory of compounds readily detected in the sediment tested, including long chain alkenones and diols, sterols, and pigments, and provide an outlook into the use of MSI in multiproxy studies.