A clinical audit is a low-cost process used for quality improvement in healthcare. Such audits are however infrequently used in resource poor countries, where the need for and potential impact of quality improvement is higher. Sets of standards for use in maternal and newborn care have been established based on internal guidelines and evidence. The before-after design of a clinical audit is prone to bias in the estimation of the impact of conducting a clinical audit. A trial design that would provide an unbiased estimate of the impact of implementing a clinical audit process on the attainment of standards selected (a standards-based audit) was needed. The aim of this paper is to introduce and describe the design of trials we developed to meet this need. A novel randomised stepped-wedge trial design to estimate the impact of conducting standards-based audits is presented. A multi-dimensional incomplete stepped-wedge cluster randomised trial design suitable for estimation of the impact of Standards-based audits on compliance with standard is proposed; two variants are described in detail. A method for sample size estimation is described. Analyses can be performed for the binary outcome using a generalised linear mixed model framework to estimate the impact of the approach on compliance with standards subjected to a standards-based audit; additional terms to consider including in sensitivity analyses are considered. The design presented has the potential to estimate the impact of introducing the standards-based audit process on compliance with standard, while providing participating healthcare providers opportunity to gain experience of implementing the standards-based audit process. The design may be applicable in other areas in which multiple processes are to be studied.