This study investigated the transition from conventional Compression Ignition (CI) to Partially Premixed Combustion (PPC) in an optical engine for fuels with differing properties. Combustion stratification and emissions were measured with diesel, naphtha and their corresponding surrogate fuels, N-heptane and PRF50. The aim of the study is to link the combustion images with engine out emissions and mixture homogeneity. Single injection strategy with the change of start of injection (SOI) from late to early injections was employed. Results show that combustion phasing trend is similar for diesel/N-heptane as well as for naphtha/PRF50 as the SOI moved from late injection timing to early injection timing. However, there is a significant difference in combustion phasing behavior for gasoline like fuels (naphtha and PRF50) and diesel fuels (diesel and N-heptane). CO emissions show an inverted V-shaped trend with one single peak in the transition zone. A “W” shape trend, with two bottoms at various dilution rates is observed for the UHC emissions. NOX emissions are high in the transition zone and decreased to lower levels in CI and PPC zones. NOX emissions are significantly reduced by reducing the intake O2 concentration with nitrogen. Except for diesel, the other three fuels show lower soot emissions. When compared to diesel like fuels, the natural luminosity of the images are lower for gasoline like fuels, indicating better premixed combustion. As the SOI is changed from CI to PPC mode, the combustion stratification increases towards a peak value in the transition zone and then decreases to a low level in PPC zone. A competition exists between the intake temperature and the dilution rate for the combustion stratification. The level of stratification is higher for real fuels (diesel and naphtha) when compared to surrogate fuel (N-heptane and PRF50).