Bio-hybrid fuels are a promising solution to accomplish a carbon-neutral and low-emission future for the transportation sector. Two potential candidates are the heterocyclic acetals 1,3-dioxane (C4H8O2) and 1,3-dioxolane (C3H6O2), which can be produced from the combination of biobased feedstocks, carbon dioxide, and renewable electricity. In this work, comprehensive experimental and numerical investigations of 1,3-dioxane and 1,3-dioxolane were performed to support their application in internal combustion engines. Ignition delay times and laminar flame speeds were measured to reveal the combustion chemistry on the macroscale, while speciation measurements in a jet-stirred reactor and ethylene-based counterflow diffusion flames provided insights into combustion chemistry and pollutant formation on the microscale. Comparing the experimental and numerical data using either available or proposed kinetic models revealed that the combustion chemistry and pollutant formation differ substantially between 1,3-dioxane and 1,3-dioxolane, although their molecular structures are similar. For example, 1,3-dioxane showed higher reactivity in the low-temperature regime (500-800 K), while 1,3-dioxolane addition to ethylene increased polycyclic aromatic hydrocarbons and soot formation in high-temperature (>800 K) counterflow diffusion flames. Reaction pathway analyses were performed to examine and explain the differences between these two bio-hybrid fuels, which originate from the chemical bond dissociation energies in their molecular structures.