To explore alternative organisational approaches used to carry out the microfinance activity, this paper compares gaps in performance of microfinance institutions (MFIs) depending on their ownership status (Privately-owned vs. NGO) and decomposes them into efficiency and technological gaps. By using a pseudo-panel Malmquist index approach to MFIs in the Latin America and Caribbean region, the selected approach overcomes the problem of different numbers of observations per year and avoids the need to pool all MFIs together to analyze group differences. Performance of MFIs is investigated from a global standpoint over the 2005-2013 period. Turning points in the performance of MFIs are closely related to recent financial crises. Privately-owned MFIs outperformed NGOs, except when the 2008- and 2011-financial crises hurt the sector. During these hard times, privately-owned companies appear less performing that NGOs, with productive frontiers most often diverging.