Boggs' early research as a PhD student was influenced by her supervisor Lawrence E. Gilbert who studied neotropical butterflies in Costa Rica and Trinidad.

Gilbert was trained by another butterfly biologist, Paul R. Ehrlich, who specializes in population ecology and whom Boggs would eventually collaborate with at Stanford University in later years.

She has also done long-term studies on temperate montane species at the Rocky Mountain Biological Laboratory, including the locally introduced Gillette's checkerspot (Euphydryas gillettii) and the Mormon fritillary (Speyeria mormonia).

Her research on S. mormonia in particular led to significant advancements in the understanding of the mechanisms underlying insect life history traits through the integration of knowledge on nutrient resource allocation.

[6][7] Boggs' research on S. mormonia in the Colorado Rocky Mountains garnered media interest in 2013 when she used over two decades of long-term data to show how climate change can affect pollinator populations,[8] raising awareness of this important issue.

In a New York Times interview, her co-author on the paper, David W. Inouye, stated that, "It is very unusual for research to uncover such a simple mechanism that can explain almost all of the variation in growth rate of an insect population".

[11] For decades, Boggs and her husband, the accomplished evolutionary biologist Ward Watt, took research students nearly every summer to the Rocky Mountain Biological Laboratory in Gothic, CO until his death in 2024.