Demand for national-level micronutrient status data continues to grow, yet little is known about the implementation of different approaches for collecting these data. We conducted an evaluation of the process of linking the 2015-2016 Malawi Demographic and Health Survey (MDHS) and 2015-2016 Malawi Micronutrient Survey (MNS). We conducted 24 in-depth interviews with stakeholders from the Malawi government and international agencies and field staff. Interview questions explored perceptions of what worked and what was challenging during three phases of implementation: preparation; data collection; and data analysis, reporting, and dissemination. Data were analysed using thematic analysis. Results showed that there was strong government interest to integrate the MDHS and MNS. Perceived benefits included potential cost savings and lower respondent burden. However, government and international agency stakeholders did not view the linkage of the surveys to be a fully integrated approach. The lack of full integration produced challenges throughout implementation, such as complex field logistics and duplication in nutrition indicators assessed and reported. Some stakeholders believed integration was not attainable primarily due to timing. The MDHS and MNS were originally designed as stand-alone surveys, and planning for each survey was at an advanced stage once the government sought to integrate the surveys. Additionally, the MNS could not be incorporated as a module within the MDHS given the complexity of the MNS data collection and short timeframe for planning. These findings can inform decisions about implementing the next MNS and may be transferable to other countries that are conducting micronutrient surveys to address data gaps.