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Obesity and pregnancy may have synergistic effects on periodontal condition, and proteomics could be an ideal approach to highlight the pathophysiological mechanisms associated with these outcomes. This study analyzed the salivary proteomics related to obesity and periodontitis in women during pregnancy (T1) and after delivery (T2). Initially, 126 women were recruited and forty were allocated into groups: with obesity and periodontitis (OP); with obesity, but without periodontitis (OWP); with normal BMI, but with periodontitis (NP); with normal BMI and without periodontitis (NWP). Whole-mouth saliva was collected in T1 and T2, and proteins were extracted and individually processed by label-free proteomics (<i>nLC-ESI-MS/MS</i>). The up-regulations of <i>Heat shock 70 kDa protein 1A</i>, <i>1B</i>, and <i>1-like</i> were related to both obesity and periodontitis, separately. <i>Albumin</i> and <i>Thioredoxin</i> were up-regulated in periodontitis cases, while <i>Cystatins</i> (mainly <i>S</i>, <i>SA</i>, <i>SN</i>) and <i>Lactotransferrin</i> were down-regulated. The high abundances of <i>Submaxillary gland androgen-regulated protein 3B</i>, <i>Protein S100-A8</i>, <i>Matrix metalloproteinase-9</i>, <i>Heat shock 70 kDa protein 2</i> and <i>6</i>, <i>Putative Heat shock 70 kDa protein 7</i>, <i>Heat shock 71 kDa protein</i>, <i>Haptoglobin</i> and <i>Plastin-1</i> were significant in the combination of obesity and periodontitis. Obesity and periodontitis remarkably altered the proteome of the saliva during pregnancy with substantial alterations after delivery.