Abstract Background To effectively deliver on proposed objectives, it is vital that practitioners, policymakers, and other stakeholders are able to clearly understand how strongly their large-scale program is being implemented. This study sought to test the feasibility, cost-effectiveness, and validity of a phone-based method as an innovative and cost-efficient approach to assessing program implementation strength (through an Implementation Strength Assessment - ISA), alternative to the traditional in-person field methods. Methods We conducted 701 mobile phone and 356 in-person interviews with facility in-Charges and two types of community health workers who provide family planning services in the Dowa and Ntcheu districts in Malawi. Responses received via the phone interview were validated through in-person review of records and inspections. Sensitivity and specificity were calculated to determine validity. Results Most indicators at the health facility and community health worker levels were above a 70% threshold for sensitivity. However, there were fewer indicators that met this threshold for specificity. The primary reason for lower specificity was due to poor recordkeeping. Collecting data via mobile phone was found to be feasible and twice as cost-efficient as collecting the same data via in-person inspections. Conclusions The rapid increase in mobile phone ownership and network availability in lower income countries could offer an alternative, cost-effective avenue to collect data for a better understanding of program implementation. Through rigorous assessment, this study found that using mobile phones could be a low-cost alternative to collect data on health system delivery of services, especially in places where routine data quality is poor and traditional, in-person methods are costly.